8.2 Pseudobulk heatmaps sorted by expression levels
- Heatmap visualization of expressed >6kbp L1HS-L1PA3 and HERVs on
pseudobulks with more than 50 nuclei (line 318).
index_row_reorder is set to the ranked TE list based on
expression values in the specific brain region (max to min
expression).
- Excluded clusters 6 (VLMC) and 7 (Tcells) due to low number of
nuclei.
asap_heatmap_snRNA(region = c("PFC"),
tes = data_TE_annotation[which(data_TE_annotation$type == "L1"),"TE_id"],
return_df = F,
breaks = seq(0,15,length.out = 52),
data = TE_data,
group_cols = c("celltype"),
index_row_reorder = c(L1s_sorted_pfc),
order_cols_groups = order_cols_celltype,
title = "PFC L1s: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
annotation_cols = annotation_cols)

## $heatmap
##
## $order_cols
## [1] "AA_ASAP90_ctrl_NP16-293_PFC_0" "AA_ASAP89_ctrl_NP16-284_PFC_0"
## [3] "AA_ASAP152_PD_NP19-91_PFC_0" "AA_ASAP116_PD_NP22-55_PFC_0"
## [5] "ASAP155_ctrl_NP23-21_PFC_0" "AA_ASAP151_PD_NP17-232_PFC_0"
## [7] "DA795_ASAP55_ctrl_NP19-37_PFC_0" "DA480_ASAP15_ctrl_NP16-21_PFC_0"
## [9] "DA430_ASAP9_PD_NP16-162_PFC_0" "DA490_ASAP11_PD_P73_PFC_0"
## [11] "AA_ASAP83_NP16-119_ctrl_PFC_0" "DA810_ASAP34_PD_NP18-304_PFC_0"
## [13] "DA428_ASAP13_ctrl_NP16-161_PFC_0" "DA488_ASAP16_ctrl_PT231_PFC_0"
## [15] "DA806_ASAP58_ctrl_NP19-45_PFC_0" "DA432_ASAP12_PD_P74_PFC_0"
## [17] "DA509_ASAP36_PD_NP19-16_PFC_0" "AA_ASAP86_NP18-148_ctrl_PFC_0"
## [19] "AA_ASAP80_PD_NP21-57_PFC_0" "DA476_ASAP10_PD_NP16-25_PFC_0"
## [21] "AA_ASAP85_NP18-46_ctrl_PFC_0" "AA_ASAP91_ctrl_NP17-20_PFC_0"
## [23] "MJ_ASAP14_ctrl_NP16-164_PFC_0" "AA_ASAP145_ctrl_NP19-218_PFC_0"
## [25] "AA_ASAP81_PD_NP21-208_PFC_0" "DA777_ASAP28_PD_NP17-191_PFC_0"
## [27] "DA499_ASAP44_PD_NP19-255_PFC_0" "DA809_ASAP30_PD_NP18-117_PFC_0"
## [29] "AA_ASAP82_PD_NP21-217_PFC_0" "AA_ASAP153_ctrl_NP19-137_PFC_0"
## [31] "DA804_ASAP49_ctrl_NP18-159_PFC_0" "DA775_ASAP22_PD_NP16-269_PFC_0"
## [33] "DA813_ASAP17_PD_NP16-140_PFC_0" "DA775_ASAP22_PD_NP16-269_PFC_1"
## [35] "DA809_ASAP30_PD_NP18-117_PFC_1" "DA804_ASAP49_ctrl_NP18-159_PFC_1"
## [37] "AA_ASAP85_NP18-46_ctrl_PFC_1" "AA_ASAP116_PD_NP22-55_PFC_1"
## [39] "MJ_ASAP14_ctrl_NP16-164_PFC_1" "AA_ASAP91_ctrl_NP17-20_PFC_1"
## [41] "ASAP155_ctrl_NP23-21_PFC_1" "DA509_ASAP36_PD_NP19-16_PFC_1"
## [43] "DA490_ASAP11_PD_P73_PFC_1" "AA_ASAP90_ctrl_NP16-293_PFC_1"
## [45] "AA_ASAP89_ctrl_NP16-284_PFC_1" "AA_ASAP152_PD_NP19-91_PFC_1"
## [47] "DA480_ASAP15_ctrl_NP16-21_PFC_1" "AA_ASAP145_ctrl_NP19-218_PFC_1"
## [49] "AA_ASAP151_PD_NP17-232_PFC_1" "AA_ASAP86_NP18-148_ctrl_PFC_1"
## [51] "DA476_ASAP10_PD_NP16-25_PFC_1" "DA430_ASAP9_PD_NP16-162_PFC_1"
## [53] "AA_ASAP83_NP16-119_ctrl_PFC_1" "AA_ASAP81_PD_NP21-208_PFC_1"
## [55] "AA_ASAP82_PD_NP21-217_PFC_1" "DA777_ASAP28_PD_NP17-191_PFC_1"
## [57] "AA_ASAP80_PD_NP21-57_PFC_1" "DA810_ASAP34_PD_NP18-304_PFC_1"
## [59] "DA806_ASAP58_ctrl_NP19-45_PFC_1" "DA499_ASAP44_PD_NP19-255_PFC_1"
## [61] "DA432_ASAP12_PD_P74_PFC_1" "DA488_ASAP16_ctrl_PT231_PFC_1"
## [63] "DA428_ASAP13_ctrl_NP16-161_PFC_1" "AA_ASAP153_ctrl_NP19-137_PFC_1"
## [65] "DA795_ASAP55_ctrl_NP19-37_PFC_1" "DA808_ASAP41_PD_NP19-108_PFC_2"
## [67] "DA775_ASAP22_PD_NP16-269_PFC_2" "DA809_ASAP30_PD_NP18-117_PFC_2"
## [69] "DA804_ASAP49_ctrl_NP18-159_PFC_2" "DA785_ASAP47_ctrl_NP17-256_PFC_2"
## [71] "AA_ASAP84_NP17-216_ctrl_PFC_2" "AA_ASAP154_ctrl_NP21-04_PFC_2"
## [73] "AA_ASAP91_ctrl_NP17-20_PFC_2" "AA_ASAP150_PD_NP16-285_PFC_2"
## [75] "MJ_ASAP14_ctrl_NP16-164_PFC_2" "DA480_ASAP15_ctrl_NP16-21_PFC_2"
## [77] "DA499_ASAP44_PD_NP19-255_PFC_2" "AA_ASAP152_PD_NP19-91_PFC_2"
## [79] "DA428_ASAP13_ctrl_NP16-161_PFC_2" "AA_ASAP153_ctrl_NP19-137_PFC_2"
## [81] "DA490_ASAP11_PD_P73_PFC_2" "AA_ASAP81_PD_NP21-208_PFC_2"
## [83] "DA432_ASAP12_PD_P74_PFC_2" "ASAP155_ctrl_NP23-21_PFC_2"
## [85] "DA509_ASAP36_PD_NP19-16_PFC_2" "AA_ASAP90_ctrl_NP16-293_PFC_2"
## [87] "AA_ASAP145_ctrl_NP19-218_PFC_2" "DA476_ASAP10_PD_NP16-25_PFC_2"
## [89] "AA_ASAP80_PD_NP21-57_PFC_2" "DA806_ASAP58_ctrl_NP19-45_PFC_2"
## [91] "DA810_ASAP34_PD_NP18-304_PFC_2" "AA_ASAP89_ctrl_NP16-284_PFC_2"
## [93] "DA430_ASAP9_PD_NP16-162_PFC_2" "AA_ASAP151_PD_NP17-232_PFC_2"
## [95] "AA_ASAP83_NP16-119_ctrl_PFC_2" "DA488_ASAP16_ctrl_PT231_PFC_2"
## [97] "AA_ASAP82_PD_NP21-217_PFC_2" "DA795_ASAP55_ctrl_NP19-37_PFC_2"
## [99] "AA_ASAP86_NP18-148_ctrl_PFC_2" "AA_ASAP116_PD_NP22-55_PFC_2"
## [101] "AA_ASAP84_NP17-216_ctrl_PFC_3" "AA_ASAP116_PD_NP22-55_PFC_3"
## [103] "AA_ASAP86_NP18-148_ctrl_PFC_3" "AA_ASAP145_ctrl_NP19-218_PFC_3"
## [105] "AA_ASAP151_PD_NP17-232_PFC_3" "DA777_ASAP28_PD_NP17-191_PFC_3"
## [107] "DA430_ASAP9_PD_NP16-162_PFC_3" "AA_ASAP83_NP16-119_ctrl_PFC_3"
## [109] "DA499_ASAP44_PD_NP19-255_PFC_3" "DA810_ASAP34_PD_NP18-304_PFC_3"
## [111] "AA_ASAP80_PD_NP21-57_PFC_3" "AA_ASAP82_PD_NP21-217_PFC_3"
## [113] "DA806_ASAP58_ctrl_NP19-45_PFC_3" "AA_ASAP150_PD_NP16-285_PFC_3"
## [115] "DA432_ASAP12_PD_P74_PFC_3" "AA_ASAP154_ctrl_NP21-04_PFC_3"
## [117] "AA_ASAP91_ctrl_NP17-20_PFC_3" "ASAP155_ctrl_NP23-21_PFC_3"
## [119] "AA_ASAP89_ctrl_NP16-284_PFC_3" "AA_ASAP152_PD_NP19-91_PFC_3"
## [121] "DA490_ASAP11_PD_P73_PFC_3" "DA480_ASAP15_ctrl_NP16-21_PFC_3"
## [123] "DA509_ASAP36_PD_NP19-16_PFC_3" "AA_ASAP90_ctrl_NP16-293_PFC_3"
## [125] "DA488_ASAP16_ctrl_PT231_PFC_3" "DA428_ASAP13_ctrl_NP16-161_PFC_3"
## [127] "DA775_ASAP22_PD_NP16-269_PFC_3" "DA785_ASAP47_ctrl_NP17-256_PFC_3"
## [129] "MJ_ASAP14_ctrl_NP16-164_PFC_3" "DA795_ASAP55_ctrl_NP19-37_PFC_3"
## [131] "DA476_ASAP10_PD_NP16-25_PFC_3" "DA804_ASAP49_ctrl_NP18-159_PFC_3"
## [133] "DA809_ASAP30_PD_NP18-117_PFC_3" "AA_ASAP154_ctrl_NP21-04_PFC_5"
## [135] "AA_ASAP84_NP17-216_ctrl_PFC_5" "DA799_ASAP19_PD_NP16-160_PFC_5"
## [137] "DA806_ASAP58_ctrl_NP19-45_PFC_5" "DA430_ASAP9_PD_NP16-162_PFC_5"
## [139] "AA_ASAP90_ctrl_NP16-293_PFC_5" "AA_ASAP83_NP16-119_ctrl_PFC_5"
## [141] "DA428_ASAP13_ctrl_NP16-161_PFC_5" "AA_ASAP85_NP18-46_ctrl_PFC_5"
## [143] "DA480_ASAP15_ctrl_NP16-21_PFC_5" "AA_ASAP152_PD_NP19-91_PFC_5"
## [145] "DA499_ASAP44_PD_NP19-255_PFC_5" "AA_ASAP80_PD_NP21-57_PFC_5"
## [147] "AA_ASAP82_PD_NP21-217_PFC_5" "DA488_ASAP16_ctrl_PT231_PFC_5"
## [149] "DA810_ASAP34_PD_NP18-304_PFC_5" "AA_ASAP86_NP18-148_ctrl_PFC_5"
## [151] "AA_ASAP145_ctrl_NP19-218_PFC_5" "MJ_ASAP14_ctrl_NP16-164_PFC_5"
## [153] "DA432_ASAP12_PD_P74_PFC_5" "DA490_ASAP11_PD_P73_PFC_5"
## [155] "DA509_ASAP36_PD_NP19-16_PFC_5" "AA_ASAP89_ctrl_NP16-284_PFC_5"
## [157] "AA_ASAP91_ctrl_NP17-20_PFC_5" "AA_ASAP153_ctrl_NP19-137_PFC_5"
## [159] "ASAP155_ctrl_NP23-21_PFC_5" "DA813_ASAP17_PD_NP16-140_PFC_5"
## [161] "DA785_ASAP47_ctrl_NP17-256_PFC_5" "DA808_ASAP41_PD_NP19-108_PFC_5"
## [163] "AA_ASAP116_PD_NP22-55_PFC_5" "AA_ASAP150_PD_NP16-285_PFC_5"
## [165] "DA777_ASAP28_PD_NP17-191_PFC_5" "AA_ASAP151_PD_NP17-232_PFC_5"
## [167] "DA476_ASAP10_PD_NP16-25_PFC_5" "DA795_ASAP55_ctrl_NP19-37_PFC_5"
## [169] "DA804_ASAP49_ctrl_NP18-159_PFC_5" "DA809_ASAP30_PD_NP18-117_PFC_5"
## [171] "DA775_ASAP22_PD_NP16-269_PFC_5" "AA_ASAP147_ctrl_NP22-37_PFC_5"
## [173] "ASAP155_ctrl_NP23-21_PFC_4" "AA_ASAP90_ctrl_NP16-293_PFC_4"
## [175] "MJ_ASAP14_ctrl_NP16-164_PFC_4" "DA499_ASAP44_PD_NP19-255_PFC_4"
## [177] "DA490_ASAP11_PD_P73_PFC_4" "DA480_ASAP15_ctrl_NP16-21_PFC_4"
## [179] "DA432_ASAP12_PD_P74_PFC_4" "AA_ASAP145_ctrl_NP19-218_PFC_4"
## [181] "AA_ASAP89_ctrl_NP16-284_PFC_4" "DA428_ASAP13_ctrl_NP16-161_PFC_4"
## [183] "AA_ASAP151_PD_NP17-232_PFC_4" "DA808_ASAP41_PD_NP19-108_PFC_4"
## [185] "DA795_ASAP55_ctrl_NP19-37_PFC_4" "DA775_ASAP22_PD_NP16-269_PFC_4"
## [187] "DA476_ASAP10_PD_NP16-25_PFC_4" "AA_ASAP86_NP18-148_ctrl_PFC_4"
## [189] "AA_ASAP83_NP16-119_ctrl_PFC_4" "DA804_ASAP49_ctrl_NP18-159_PFC_4"
## [191] "DA806_ASAP58_ctrl_NP19-45_PFC_4" "AA_ASAP152_PD_NP19-91_PFC_4"
## [193] "AA_ASAP80_PD_NP21-57_PFC_4" "AA_ASAP82_PD_NP21-217_PFC_4"
## [195] "DA488_ASAP16_ctrl_PT231_PFC_4" "DA430_ASAP9_PD_NP16-162_PFC_4"
## [197] "AA_ASAP116_PD_NP22-55_PFC_4" "DA428_ASAP13_ctrl_NP16-161_PFC_6"
## [199] "AA_ASAP89_ctrl_NP16-284_PFC_6" "AA_ASAP152_PD_NP19-91_PFC_6"
## [201] "MJ_ASAP14_ctrl_NP16-164_PFC_6" "DA785_ASAP47_ctrl_NP17-256_PFC_6"
##
## $order_rows
## [1] "L1PA2_dup1230" "L1PA2_dup848" "L1PA2_dup791" "L1HS_dup1462"
## [5] "L1PA2_dup4403" "L1PA3_dup398" "L1PA2_dup585" "L1PA2_dup513"
## [9] "L1PA3_dup10686" "L1HS_dup337" "L1PA3_dup1010" "L1PA3_dup4994"
## [13] "L1PA3_dup8173" "L1PA2_dup663" "L1PA2_dup234" "L1HS_dup124"
## [17] "L1PA3_dup2557" "L1HS_dup455" "L1PA3_dup8903" "L1PA3_dup10285"
## [21] "L1PA3_dup2204" "L1PA2_dup4651" "L1PA2_dup2245" "L1PA2_dup922"
## [25] "L1PA2_dup378" "L1PA3_dup7864" "L1PA3_dup761" "L1PA3_dup10119"
## [29] "L1PA2_dup1621" "L1PA3_dup2413" "L1PA3_dup4492" "L1PA3_dup2744"
## [33] "L1PA2_dup3736" "L1PA2_dup4074" "L1PA3_dup10297" "L1PA2_dup37"
## [37] "L1PA2_dup1462" "L1HS_dup1324" "L1PA3_dup400" "L1PA3_dup4888"
## [41] "L1PA3_dup8663" "L1PA2_dup949" "L1PA3_dup527" "L1PA3_dup1651"
## [45] "L1PA3_dup9021" "L1PA2_dup39" "L1PA2_dup4838" "L1PA3_dup3102"
## [49] "L1PA3_dup1710" "L1PA3_dup5928" "L1PA3_dup9430" "L1PA2_dup4612"
## [53] "L1PA3_dup8872" "L1PA2_dup1298" "L1PA3_dup8522" "L1PA3_dup2517"
## [57] "L1PA3_dup1" "L1PA2_dup559" "L1PA3_dup4668" "L1PA3_dup2919"
## [61] "L1PA3_dup872" "L1PA3_dup4118" "L1PA3_dup748" "L1PA2_dup2504"
## [65] "L1PA3_dup10072" "L1PA3_dup5337" "L1PA3_dup6385" "L1PA2_dup927"
## [69] "L1PA3_dup4393" "L1HS_dup444" "L1PA3_dup1756" "L1HS_dup916"
## [73] "L1PA3_dup4891" "L1PA3_dup4709" "L1PA3_dup6929" "L1HS_dup514"
## [77] "L1PA2_dup2720" "L1PA2_dup2047" "L1PA2_dup1379" "L1PA2_dup2408"
## [81] "L1PA2_dup4620" "L1PA3_dup9946" "L1HS_dup788" "L1PA2_dup109"
## [85] "L1PA3_dup8007" "L1PA3_dup1428" "L1PA3_dup9280" "L1PA3_dup2593"
## [89] "L1PA2_dup4430" "L1PA2_dup2091" "L1PA2_dup526" "L1PA3_dup529"
## [93] "L1PA2_dup3484" "L1PA2_dup2289" "L1PA3_dup3168" "L1PA2_dup4936"
## [97] "L1HS_dup1014" "L1PA3_dup1311" "L1HS_dup1330" "L1PA3_dup8420"
## [101] "L1PA3_dup373" "L1PA3_dup8506" "L1PA2_dup410" "L1PA3_dup2760"
## [105] "L1PA2_dup2343" "L1PA3_dup10740" "L1PA2_dup3425" "L1HS_dup1182"
## [109] "L1PA2_dup4053" "L1PA2_dup1953" "L1PA3_dup2551" "L1PA2_dup2791"
## [113] "L1PA3_dup1723" "L1PA2_dup4901" "L1PA2_dup1398" "L1PA2_dup737"
## [117] "L1PA2_dup2680" "L1PA3_dup7470" "L1PA2_dup3292" "L1PA2_dup423"
## [121] "L1PA3_dup7605" "L1PA2_dup142" "L1HS_dup35" "L1PA3_dup10525"
## [125] "L1HS_dup138" "L1PA3_dup4277" "L1PA3_dup3954" "L1PA2_dup3771"
## [129] "L1PA2_dup3607" "L1PA3_dup1988" "L1PA3_dup5514" "L1PA3_dup6008"
## [133] "L1PA3_dup6147" "L1PA2_dup2385" "L1HS_dup1357" "L1PA3_dup6002"
## [137] "L1PA2_dup662" "L1PA2_dup3136" "L1PA3_dup3758" "L1PA2_dup4775"
## [141] "L1PA2_dup3589" "L1PA3_dup6457" "L1PA3_dup4804" "L1PA3_dup5680"
## [145] "L1PA3_dup3484" "L1PA3_dup1547" "L1PA3_dup2393" "L1PA2_dup1476"
## [149] "L1HS_dup240" "L1PA2_dup130" "L1PA2_dup2969" "L1PA3_dup3586"
## [153] "L1HS_dup429" "L1PA3_dup6317" "L1HS_dup449" "L1PA2_dup3773"
## [157] "L1HS_dup62" "L1HS_dup649" "L1PA3_dup3323" "L1PA3_dup2272"
## [161] "L1PA3_dup2721" "L1PA2_dup4335" "L1HS_dup370" "L1PA2_dup1490"
## [165] "L1HS_dup1339" "L1PA2_dup200" "L1PA3_dup9734" "L1PA2_dup2180"
## [169] "L1PA3_dup358" "L1PA3_dup7821" "L1PA3_dup6036" "L1PA2_dup3531"
## [173] "L1PA3_dup5121" "L1PA2_dup2863" "L1PA2_dup2164" "L1PA2_dup1760"
## [177] "L1PA3_dup5866" "L1HS_dup995" "L1PA3_dup5106" "L1PA3_dup561"
## [181] "L1HS_dup163" "L1HS_dup379" "L1PA2_dup2909" "L1PA3_dup1550"
## [185] "L1PA3_dup2389" "L1HS_dup111" "L1PA2_dup4548" "L1PA2_dup3805"
## [189] "L1PA3_dup7862" "L1PA2_dup678" "L1PA3_dup4487" "L1PA2_dup1770"
## [193] "L1PA3_dup9373" "L1PA3_dup8520" "L1PA2_dup741" "L1PA2_dup1653"
## [197] "L1PA3_dup9256" "L1PA3_dup4885" "L1PA2_dup4030" "L1PA3_dup1528"
## [201] "L1PA3_dup2357" "L1PA2_dup16" "L1HS_dup1536" "L1PA3_dup9473"
## [205] "L1PA3_dup1937" "L1PA3_dup7947" "L1PA3_dup128" "L1PA2_dup3742"
## [209] "L1PA2_dup4421" "L1HS_dup879" "L1PA2_dup1560" "L1PA2_dup4262"
## [213] "L1HS_dup1104" "L1PA3_dup6434" "L1PA2_dup675" "L1PA3_dup3863"
## [217] "L1PA3_dup8525" "L1HS_dup948" "L1PA3_dup9095" "L1PA3_dup5745"
## [221] "L1PA3_dup10011" "L1PA2_dup2506" "L1PA3_dup1114" "L1PA3_dup3763"
## [225] "L1PA3_dup1770" "L1PA2_dup1778" "L1PA2_dup935" "L1PA3_dup1800"
## [229] "L1PA3_dup4603" "L1PA3_dup8891" "L1PA2_dup4226" "L1PA3_dup3306"
## [233] "L1PA3_dup1554" "L1PA3_dup3404" "L1PA3_dup6692" "L1PA2_dup3664"
## [237] "L1PA3_dup2662" "L1PA3_dup5534" "L1HS_dup244" "L1HS_dup632"
## [241] "L1PA3_dup5207" "L1PA2_dup4440" "L1PA3_dup8571" "L1PA3_dup4884"
## [245] "L1HS_dup1478" "L1PA2_dup4596" "L1PA3_dup6436" "L1PA3_dup3941"
## [249] "L1HS_dup191" "L1PA3_dup9702" "L1PA3_dup7951" "L1PA2_dup1752"
## [253] "L1PA3_dup1264" "L1PA2_dup1933" "L1PA3_dup3968" "L1HS_dup1286"
## [257] "L1HS_dup579" "L1PA3_dup978" "L1PA3_dup6550" "L1PA2_dup3437"
## [261] "L1PA2_dup2860" "L1PA3_dup7637" "L1PA2_dup1112" "L1PA3_dup5047"
## [265] "L1PA2_dup221" "L1HS_dup270" "L1PA2_dup1331" "L1HS_dup405"
## [269] "L1PA2_dup4043" "L1PA2_dup2155" "L1PA2_dup1749" "L1PA3_dup345"
## [273] "L1PA3_dup3757" "L1PA3_dup4349" "L1PA2_dup360" "L1HS_dup1393"
## [277] "L1PA2_dup595" "L1PA3_dup2954" "L1PA3_dup6573" "L1PA2_dup4714"
## [281] "L1HS_dup1020" "L1PA2_dup4441" "L1HS_dup1473" "L1PA3_dup9202"
## [285] "L1PA2_dup3405" "L1PA2_dup4045" "L1PA2_dup71" "L1PA3_dup7963"
## [289] "L1PA2_dup2254" "L1PA3_dup4391" "L1PA3_dup10344" "L1HS_dup1514"
## [293] "L1PA3_dup4401" "L1PA3_dup247" "L1PA2_dup365" "L1PA3_dup7840"
## [297] "L1PA2_dup1426" "L1PA2_dup994" "L1HS_dup1284" "L1PA3_dup907"
## [301] "L1PA2_dup1805" "L1PA3_dup3729" "L1HS_dup1342" "L1PA2_dup1049"
## [305] "L1PA3_dup5468" "L1PA2_dup4686" "L1PA2_dup4611" "L1PA2_dup4522"
## [309] "L1HS_dup596" "L1PA2_dup727" "L1PA2_dup3283" "L1PA3_dup7237"
## [313] "L1PA3_dup3307" "L1HS_dup1019" "L1PA3_dup4408" "L1PA2_dup2444"
## [317] "L1PA2_dup3579" "L1HS_dup800" "L1PA2_dup3042" "L1PA3_dup7472"
## [321] "L1PA3_dup3959" "L1HS_dup155" "L1PA2_dup635" "L1PA3_dup5510"
## [325] "L1PA2_dup3445" "L1PA3_dup7550" "L1PA2_dup4237" "L1PA2_dup1177"
## [329] "L1PA3_dup5544" "L1HS_dup1077" "L1PA2_dup326" "L1PA3_dup4708"
## [333] "L1HS_dup811" "L1PA3_dup10096" "L1PA2_dup383" "L1PA3_dup9856"
## [337] "L1PA2_dup2295" "L1PA2_dup4639" "L1PA3_dup124" "L1PA2_dup4762"
## [341] "L1PA2_dup3615" "L1PA2_dup3930" "L1PA3_dup6387" "L1PA2_dup98"
## [345] "L1HS_dup907" "L1PA2_dup1058" "L1PA3_dup2620" "L1PA2_dup196"
## [349] "L1PA3_dup3291" "L1PA2_dup2436" "L1PA2_dup1746" "L1HS_dup90"
## [353] "L1HS_dup803" "L1PA2_dup4528" "L1PA2_dup4776" "L1PA2_dup4367"
## [357] "L1PA3_dup6160" "L1PA3_dup3684" "L1PA2_dup2565" "L1PA2_dup4378"
## [361] "L1HS_dup831" "L1HS_dup1005" "L1PA3_dup4902" "L1PA3_dup3509"
## [365] "L1HS_dup143" "L1PA2_dup629" "L1PA3_dup3502" "L1PA3_dup1463"
## [369] "L1PA2_dup4309" "L1PA3_dup6347" "L1PA2_dup3503" "L1PA2_dup2988"
## [373] "L1PA3_dup3507" "L1PA3_dup2643" "L1PA3_dup5594" "L1PA2_dup3439"
## [377] "L1HS_dup225" "L1PA2_dup530" "L1PA3_dup165" "L1PA2_dup514"
## [381] "L1PA2_dup382" "L1PA3_dup1269" "L1PA3_dup7432" "L1HS_dup204"
## [385] "L1PA2_dup732" "L1PA2_dup4196" "L1PA2_dup4652" "L1PA2_dup2271"
## [389] "L1PA2_dup759" "L1PA3_dup3880" "L1PA2_dup3776" "L1PA3_dup5355"
## [393] "L1PA3_dup8310" "L1HS_dup1295" "L1PA3_dup8328" "L1PA3_dup1337"
## [397] "L1PA2_dup413" "L1PA3_dup5886" "L1HS_dup679" "L1PA2_dup2729"
## [401] "L1PA2_dup684" "L1PA2_dup1023" "L1PA2_dup1050" "L1PA2_dup1272"
## [405] "L1PA3_dup3300" "L1PA3_dup5927" "L1HS_dup87" "L1HS_dup743"
## [409] "L1HS_dup1576" "L1PA3_dup5238" "L1HS_dup622" "L1PA3_dup2683"
## [413] "L1HS_dup1616" "L1PA2_dup4454" "L1PA2_dup726" "L1PA2_dup1968"
## [417] "L1PA3_dup9998" "L1PA2_dup4905" "L1PA2_dup4791" "L1PA3_dup4688"
## [421] "L1PA2_dup4618" "L1HS_dup1437" "L1PA2_dup2496" "L1PA2_dup3160"
## [425] "L1PA2_dup358" "L1PA2_dup3622" "L1PA3_dup5057" "L1PA3_dup1727"
## [429] "L1PA3_dup1046" "L1PA3_dup10531" "L1PA2_dup3426" "L1PA2_dup747"
## [433] "L1PA3_dup5358" "L1PA3_dup6966" "L1PA3_dup1027" "L1PA3_dup1989"
## [437] "L1PA3_dup4122" "L1PA2_dup1978" "L1PA2_dup219" "L1PA2_dup1463"
## [441] "L1PA3_dup6884" "L1PA3_dup6584" "L1HS_dup787" "L1HS_dup802"
## [445] "L1PA3_dup2039" "L1PA3_dup3005" "L1PA3_dup4596" "L1PA2_dup4478"
## [449] "L1HS_dup1243" "L1PA2_dup2876" "L1PA2_dup2537" "L1PA3_dup6523"
## [453] "L1PA2_dup805" "L1PA3_dup6730" "L1PA2_dup4201" "L1PA3_dup7792"
## [457] "L1PA2_dup2127" "L1PA3_dup4259" "L1PA2_dup589" "L1PA2_dup1248"
## [461] "L1PA3_dup7316" "L1PA3_dup5418" "L1PA2_dup4389" "L1PA3_dup9840"
## [465] "L1PA3_dup9722" "L1PA2_dup2577" "L1PA3_dup5540" "L1PA3_dup9866"
## [469] "L1PA2_dup3003" "L1PA3_dup8896" "L1PA3_dup1328" "L1HS_dup376"
## [473] "L1PA3_dup3153" "L1PA2_dup4432" "L1HS_dup1491" "L1PA2_dup472"
## [477] "L1PA2_dup3881" "L1HS_dup466" "L1PA2_dup1418" "L1PA3_dup10176"
## [481] "L1PA2_dup2168" "L1PA2_dup2089" "L1PA2_dup2282" "L1PA3_dup2755"
## [485] "L1PA2_dup2004" "L1HS_dup1501" "L1PA2_dup1078" "L1PA3_dup5363"
## [489] "L1PA3_dup638" "L1PA3_dup7893" "L1HS_dup600" "L1PA3_dup6112"
## [493] "L1PA2_dup2261" "L1PA3_dup8117" "L1PA2_dup2581" "L1PA2_dup3118"
## [497] "L1PA2_dup3766" "L1PA3_dup1647" "L1PA3_dup840" "L1PA3_dup1279"
## [501] "L1PA3_dup1952" "L1PA2_dup3629" "L1PA3_dup1026" "L1PA3_dup8313"
## [505] "L1PA3_dup7288" "L1PA2_dup798" "L1PA2_dup2430" "L1PA2_dup4713"
## [509] "L1PA2_dup1375" "L1PA2_dup307" "L1PA3_dup4687" "L1PA3_dup5825"
## [513] "L1PA3_dup1943" "L1PA2_dup1992" "L1PA3_dup10043" "L1PA3_dup6871"
## [517] "L1PA3_dup3950" "L1PA3_dup683" "L1PA2_dup4688" "L1PA3_dup9255"
asap_heatmap_snRNA(region = c("PUT"),
tes = data_TE_annotation[which(data_TE_annotation$type == "L1"),"TE_id"],
return_df = F,
breaks = seq(0,15,length.out = 52),
data = TE_data,
group_cols = c("celltype"),
index_row_reorder = c(L1s_sorted_put),
order_cols_groups = order_cols_celltype,
title = "PUT L1s: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
annotation_cols = annotation_cols)

## $heatmap
##
## $order_cols
## [1] "AA_ASAP138_PD_NP16-285_PUT_0" "AA79_ASAP64_PD_NP16-162_PUT_0"
## [3] "AA84_ASAP71_PD_NP19-16_PUT_0" "AA_ASAP100_ctrl_NP18-148_PUT_0"
## [5] "AA_ASAP97_PD_NP21-57_PUT_0" "AA_ASAP141_ctrl_NP19-218_PUT_0"
## [7] "AA87_ASAP76_ctrl_NP18-159_PUT_0" "AA71_ASAP70_PD_NP18-304_PUT_0"
## [9] "AA_ASAP98_ctrl_NP16-119_PUT_0" "AA74_ASAP62_PD_NP16-140_PUT_0"
## [11] "AA82_ASAP68_PD_NP18-117_PUT_0" "AA87_ASAP76_ctrl_NP18-159_PUT_1"
## [13] "AA_ASAP100_ctrl_NP18-148_PUT_1" "AA79_ASAP64_PD_NP16-162_PUT_1"
## [15] "AA71_ASAP70_PD_NP18-304_PUT_1" "AA74_ASAP62_PD_NP16-140_PUT_1"
## [17] "AA84_ASAP71_PD_NP19-16_PUT_1" "AA_ASAP139_PD_NP17-232_PUT_1"
## [19] "AA_ASAP144_PD_NP19-137_PUT_1" "AA_ASAP92_ctrl_NP16-284_PUT_1"
## [21] "AA_ASAP117_PD_NP22-55_PUT_1" "AA_ASAP87_PD_NP21-208_PUT_1"
## [23] "AA_ASAP88_PD_NP21-217_PUT_1" "AA89_ASAP78_ctrl_NP19-37_PUT_2"
## [25] "AA88_ASAP77_ctrl_NP19-36_PUT_2" "AA_ASAP96_ctrl_NP18-46_PUT_2"
## [27] "AA76_ASAP74_PD_NP19-255_PUT_2" "AA_ASAP94_ctrl_NP17-20_PUT_2"
## [29] "AA86_ASAP73_PD_NP19-108_PUT_2" "AA_ASAP92_ctrl_NP16-284_PUT_2"
## [31] "AA_ASAP146_PD_NP21-04_PUT_2" "AA_ASAP88_PD_NP21-217_PUT_2"
## [33] "AA_ASAP139_PD_NP17-232_PUT_2" "AA_ASAP93_ctrl_NP16-293_PUT_2"
## [35] "AA_ASAP98_ctrl_NP16-119_PUT_2" "AA_ASAP138_PD_NP16-285_PUT_2"
## [37] "AA84_ASAP71_PD_NP19-16_PUT_2" "AA_ASAP97_PD_NP21-57_PUT_2"
## [39] "AA_ASAP87_PD_NP21-208_PUT_2" "AA74_ASAP62_PD_NP16-140_PUT_2"
## [41] "AA71_ASAP70_PD_NP18-304_PUT_2" "AA85_ASAP72_PD_NP19-23_PUT_2"
## [43] "AA73_ASAP65_PD_NP16-269_PUT_2" "AA82_ASAP68_PD_NP18-117_PUT_2"
## [45] "AA77_ASAP61_PD_NP16-25_PUT_2" "AA79_ASAP64_PD_NP16-162_PUT_2"
## [47] "AA_ASAP144_PD_NP19-137_PUT_2" "AA_ASAP117_PD_NP22-55_PUT_2"
## [49] "AA_ASAP100_ctrl_NP18-148_PUT_2" "AA87_ASAP76_ctrl_NP18-159_PUT_2"
## [51] "AA83_ASAP69_PD_NP18-287_PUT_2" "AA81_ASAP67_PD_NP17-191_PUT_2"
## [53] "AA_ASAP141_ctrl_NP19-218_PUT_2" "AA_ASAP140_PD_NP19-91_PUT_2"
## [55] "AA_ASAP149_PD_NP23-21_PUT_3" "AA74_ASAP62_PD_NP16-140_PUT_3"
## [57] "AA_ASAP141_ctrl_NP19-218_PUT_3" "AA84_ASAP71_PD_NP19-16_PUT_3"
## [59] "AA79_ASAP64_PD_NP16-162_PUT_3" "AA_ASAP100_ctrl_NP18-148_PUT_3"
## [61] "AA_ASAP144_PD_NP19-137_PUT_3" "AA_ASAP139_PD_NP17-232_PUT_3"
## [63] "AA_ASAP138_PD_NP16-285_PUT_3" "AA_ASAP117_PD_NP22-55_PUT_3"
## [65] "AA_ASAP93_ctrl_NP16-293_PUT_3" "AA85_ASAP72_PD_NP19-23_PUT_3"
## [67] "AA_ASAP140_PD_NP19-91_PUT_3" "AA86_ASAP73_PD_NP19-108_PUT_3"
## [69] "AA_ASAP142_ctrl_NP22-37_PUT_3" "AA_ASAP94_ctrl_NP17-20_PUT_3"
## [71] "AA89_ASAP78_ctrl_NP19-37_PUT_3" "AA73_ASAP65_PD_NP16-269_PUT_3"
## [73] "AA81_ASAP67_PD_NP17-191_PUT_3" "AA_ASAP146_PD_NP21-04_PUT_3"
## [75] "AA76_ASAP74_PD_NP19-255_PUT_3" "AA_ASAP92_ctrl_NP16-284_PUT_3"
## [77] "AA77_ASAP61_PD_NP16-25_PUT_3" "AA71_ASAP70_PD_NP18-304_PUT_3"
## [79] "AA83_ASAP69_PD_NP18-287_PUT_3" "AA82_ASAP68_PD_NP18-117_PUT_3"
## [81] "AA_ASAP88_PD_NP21-217_PUT_3" "AA88_ASAP77_ctrl_NP19-36_PUT_3"
## [83] "AA_ASAP87_PD_NP21-208_PUT_3" "AA_ASAP97_PD_NP21-57_PUT_3"
## [85] "AA87_ASAP76_ctrl_NP18-159_PUT_3" "AA_ASAP98_ctrl_NP16-119_PUT_3"
## [87] "AA_ASAP96_ctrl_NP18-46_PUT_3" "AA_ASAP92_ctrl_NP16-284_PUT_5"
## [89] "AA_ASAP146_PD_NP21-04_PUT_5" "AA_ASAP87_PD_NP21-208_PUT_5"
## [91] "AA_ASAP140_PD_NP19-91_PUT_5" "AA_ASAP141_ctrl_NP19-218_PUT_5"
## [93] "AA_ASAP100_ctrl_NP18-148_PUT_5" "AA_ASAP144_PD_NP19-137_PUT_5"
## [95] "AA_ASAP97_PD_NP21-57_PUT_5" "AA87_ASAP76_ctrl_NP18-159_PUT_5"
## [97] "AA84_ASAP71_PD_NP19-16_PUT_5" "AA_ASAP138_PD_NP16-285_PUT_5"
## [99] "AA_ASAP139_PD_NP17-232_PUT_5" "AA_ASAP88_PD_NP21-217_PUT_5"
## [101] "AA_ASAP98_ctrl_NP16-119_PUT_5" "AA79_ASAP64_PD_NP16-162_PUT_5"
## [103] "AA_ASAP117_PD_NP22-55_PUT_5" "AA_ASAP96_ctrl_NP18-46_PUT_5"
## [105] "AA71_ASAP70_PD_NP18-304_PUT_5" "AA86_ASAP73_PD_NP19-108_PUT_5"
## [107] "AA_ASAP94_ctrl_NP17-20_PUT_5" "AA89_ASAP78_ctrl_NP19-37_PUT_5"
## [109] "AA88_ASAP77_ctrl_NP19-36_PUT_5" "AA85_ASAP72_PD_NP19-23_PUT_5"
## [111] "AA74_ASAP62_PD_NP16-140_PUT_5" "AA_ASAP93_ctrl_NP16-293_PUT_5"
## [113] "AA82_ASAP68_PD_NP18-117_PUT_5" "AA77_ASAP61_PD_NP16-25_PUT_5"
## [115] "AA83_ASAP69_PD_NP18-287_PUT_5" "AA81_ASAP67_PD_NP17-191_PUT_5"
## [117] "AA73_ASAP65_PD_NP16-269_PUT_5" "AA_ASAP142_ctrl_NP22-37_PUT_5"
## [119] "AA76_ASAP74_PD_NP19-255_PUT_5" "AA_ASAP149_PD_NP23-21_PUT_5"
## [121] "AA78_ASAP63_PD_NP16-160_PUT_5" "AA89_ASAP78_ctrl_NP19-37_PUT_4"
## [123] "AA_ASAP94_ctrl_NP17-20_PUT_4" "AA_ASAP96_ctrl_NP18-46_PUT_4"
## [125] "AA_ASAP138_PD_NP16-285_PUT_4" "AA_ASAP141_ctrl_NP19-218_PUT_4"
## [127] "AA_ASAP140_PD_NP19-91_PUT_4" "AA79_ASAP64_PD_NP16-162_PUT_4"
## [129] "AA73_ASAP65_PD_NP16-269_PUT_4" "AA85_ASAP72_PD_NP19-23_PUT_4"
## [131] "AA77_ASAP61_PD_NP16-25_PUT_4" "AA76_ASAP74_PD_NP19-255_PUT_4"
## [133] "AA83_ASAP69_PD_NP18-287_PUT_4" "AA81_ASAP67_PD_NP17-191_PUT_4"
## [135] "AA74_ASAP62_PD_NP16-140_PUT_4" "AA71_ASAP70_PD_NP18-304_PUT_4"
## [137] "AA_ASAP88_PD_NP21-217_PUT_4" "AA_ASAP87_PD_NP21-208_PUT_4"
## [139] "AA_ASAP117_PD_NP22-55_PUT_4" "AA_ASAP97_PD_NP21-57_PUT_4"
## [141] "AA87_ASAP76_ctrl_NP18-159_PUT_4" "AA_ASAP100_ctrl_NP18-148_PUT_4"
## [143] "AA_ASAP144_PD_NP19-137_PUT_4" "AA84_ASAP71_PD_NP19-16_PUT_4"
## [145] "AA_ASAP98_ctrl_NP16-119_PUT_4"
##
## $order_rows
## [1] "L1PA2_dup791" "L1PA2_dup848" "L1PA2_dup1230" "L1HS_dup1462"
## [5] "L1PA3_dup1010" "L1PA3_dup10686" "L1PA2_dup4403" "L1PA2_dup585"
## [9] "L1PA3_dup398" "L1HS_dup1324" "L1HS_dup124" "L1PA3_dup2557"
## [13] "L1PA3_dup8903" "L1PA3_dup4994" "L1PA2_dup234" "L1PA2_dup663"
## [17] "L1HS_dup337" "L1PA2_dup922" "L1PA3_dup10285" "L1PA2_dup378"
## [21] "L1PA3_dup8173" "L1PA3_dup2744" "L1PA2_dup949" "L1PA3_dup10297"
## [25] "L1PA2_dup4651" "L1PA2_dup3736" "L1PA3_dup8420" "L1PA2_dup4713"
## [29] "L1PA3_dup10119" "L1PA2_dup513" "L1PA2_dup2408" "L1PA3_dup4492"
## [33] "L1PA2_dup2720" "L1PA2_dup1621" "L1PA3_dup2413" "L1PA3_dup2204"
## [37] "L1PA2_dup39" "L1HS_dup455" "L1PA3_dup2919" "L1PA3_dup6008"
## [41] "L1PA3_dup4888" "L1PA2_dup526" "L1PA2_dup927" "L1PA3_dup1264"
## [45] "L1PA2_dup1462" "L1PA3_dup4118" "L1PA3_dup4668" "L1PA3_dup5337"
## [49] "L1PA3_dup400" "L1PA3_dup9095" "L1PA3_dup1710" "L1PA2_dup3664"
## [53] "L1PA3_dup1651" "L1PA3_dup2517" "L1PA3_dup5106" "L1PA3_dup4277"
## [57] "L1HS_dup1014" "L1PA3_dup1" "L1PA3_dup872" "L1PA3_dup2760"
## [61] "L1PA3_dup2393" "L1PA3_dup8522" "L1PA2_dup2245" "L1PA3_dup4891"
## [65] "L1HS_dup787" "L1PA2_dup4596" "L1PA2_dup2680" "L1PA3_dup9280"
## [69] "L1PA3_dup527" "L1HS_dup916" "L1PA2_dup559" "L1PA2_dup3607"
## [73] "L1PA3_dup3102" "L1PA3_dup8663" "L1PA2_dup2791" "L1PA3_dup358"
## [77] "L1PA2_dup142" "L1PA3_dup3168" "L1PA3_dup1800" "L1PA3_dup3757"
## [81] "L1PA2_dup4791" "L1HS_dup1330" "L1PA2_dup4237" "L1PA3_dup1311"
## [85] "L1PA3_dup6002" "L1PA2_dup423" "L1PA2_dup2343" "L1PA3_dup761"
## [89] "L1PA3_dup1770" "L1PA3_dup9430" "L1PA3_dup6385" "L1PA3_dup8872"
## [93] "L1PA2_dup1953" "L1PA2_dup4620" "L1PA2_dup2289" "L1PA2_dup1298"
## [97] "L1PA3_dup6884" "L1PA3_dup10525" "L1PA3_dup8007" "L1PA2_dup2969"
## [101] "L1PA2_dup2091" "L1PA3_dup2593" "L1PA2_dup4074" "L1PA3_dup9946"
## [105] "L1PA2_dup1398" "L1PA2_dup675" "L1PA3_dup1547" "L1PA3_dup5928"
## [109] "L1PA2_dup662" "L1PA2_dup727" "L1PA2_dup1752" "L1PA3_dup8506"
## [113] "L1PA3_dup3153" "L1PA2_dup4936" "L1PA3_dup1756" "L1PA3_dup3729"
## [117] "L1PA3_dup6966" "L1HS_dup649" "L1PA3_dup529" "L1PA3_dup6457"
## [121] "L1PA2_dup3771" "L1PA2_dup3425" "L1HS_dup240" "L1HS_dup138"
## [125] "L1PA3_dup9856" "L1PA3_dup7864" "L1PA3_dup7470" "L1PA2_dup2164"
## [129] "L1PA3_dup5121" "L1PA3_dup3586" "L1HS_dup379" "L1PA3_dup5534"
## [133] "L1PA2_dup3589" "L1PA3_dup4709" "L1PA2_dup3531" "L1PA2_dup1272"
## [137] "L1PA2_dup3484" "L1PA2_dup935" "L1PA2_dup2909" "L1PA3_dup6317"
## [141] "L1HS_dup449" "L1PA3_dup561" "L1PA3_dup9021" "L1PA3_dup1988"
## [145] "L1PA2_dup4367" "L1PA3_dup373" "L1PA2_dup2860" "L1PA2_dup4053"
## [149] "L1HS_dup155" "L1PA2_dup4905" "L1PA3_dup1428" "L1PA3_dup4401"
## [153] "L1PA3_dup10740" "L1HS_dup444" "L1PA3_dup9473" "L1PA2_dup3437"
## [157] "L1PA2_dup3136" "L1PA3_dup3758" "L1HS_dup788" "L1HS_dup1182"
## [161] "L1PA2_dup2155" "L1PA2_dup71" "L1PA3_dup7862" "L1PA3_dup9256"
## [165] "L1PA3_dup6036" "L1PA3_dup683" "L1PA2_dup1379" "L1PA3_dup978"
## [169] "L1HS_dup1339" "L1PA3_dup6147" "L1PA2_dup994" "L1HS_dup596"
## [173] "L1PA2_dup4639" "L1PA2_dup2504" "L1PA2_dup1778" "L1HS_dup632"
## [177] "L1PA3_dup3763" "L1PA2_dup798" "L1HS_dup1616" "L1PA2_dup1490"
## [181] "L1PA2_dup4775" "L1PA2_dup109" "L1HS_dup1286" "L1HS_dup429"
## [185] "L1PA3_dup7821" "L1PA3_dup9840" "L1PA3_dup7605" "L1PA2_dup2047"
## [189] "L1HS_dup1536" "L1PA2_dup3579" "L1HS_dup111" "L1PA2_dup4262"
## [193] "L1PA2_dup2863" "L1PA3_dup3863" "L1PA3_dup3507" "L1HS_dup514"
## [197] "L1PA2_dup410" "L1PA3_dup10344" "L1PA3_dup10531" "L1PA3_dup3941"
## [201] "L1PA3_dup10011" "L1PA3_dup1937" "L1PA3_dup4885" "L1PA2_dup3805"
## [205] "L1PA3_dup165" "L1PA3_dup5047" "L1PA3_dup5680" "L1PA3_dup7951"
## [209] "L1PA3_dup2272" "L1PA3_dup1723" "L1PA3_dup2643" "L1PA2_dup4548"
## [213] "L1PA2_dup805" "L1PA3_dup9734" "L1PA3_dup4804" "L1HS_dup1019"
## [217] "L1PA2_dup4838" "L1PA2_dup37" "L1PA2_dup759" "L1PA3_dup2721"
## [221] "L1PA3_dup7472" "L1PA2_dup1426" "L1PA3_dup5514" "L1PA3_dup3306"
## [225] "L1PA2_dup737" "L1PA2_dup4714" "L1PA2_dup3292" "L1PA3_dup128"
## [229] "L1PA2_dup200" "L1PA2_dup3615" "L1PA2_dup4686" "L1PA2_dup595"
## [233] "L1PA2_dup1050" "L1PA2_dup3503" "L1PA2_dup130" "L1PA2_dup4196"
## [237] "L1PA2_dup4762" "L1PA3_dup3484" "L1PA3_dup7637" "L1PA3_dup5510"
## [241] "L1PA3_dup4688" "L1PA2_dup4309" "L1PA2_dup1749" "L1PA3_dup9373"
## [245] "L1PA2_dup4901" "L1PA2_dup2180" "L1PA3_dup2357" "L1PA2_dup1968"
## [249] "L1PA3_dup7237" "L1PA3_dup6692" "L1PA2_dup1331" "L1PA2_dup2254"
## [253] "L1PA2_dup16" "L1HS_dup191" "L1PA2_dup4030" "L1PA2_dup4440"
## [257] "L1PA2_dup2261" "L1PA3_dup8117" "L1PA3_dup6550" "L1PA3_dup2551"
## [261] "L1HS_dup370" "L1HS_dup995" "L1PA3_dup6347" "L1PA3_dup6436"
## [265] "L1PA2_dup1770" "L1PA2_dup3405" "L1HS_dup405" "L1PA3_dup5363"
## [269] "L1PA2_dup221" "L1PA3_dup3968" "L1PA3_dup8520" "L1PA3_dup2620"
## [273] "L1PA3_dup6573" "L1PA3_dup3954" "L1HS_dup679" "L1PA2_dup684"
## [277] "L1PA3_dup2389" "L1PA3_dup4902" "L1PA2_dup3742" "L1PA2_dup2496"
## [281] "L1PA3_dup10176" "L1PA2_dup1992" "L1PA2_dup4421" "L1PA2_dup4652"
## [285] "L1PA3_dup3509" "L1PA2_dup629" "L1PA3_dup10096" "L1PA3_dup748"
## [289] "L1HS_dup376" "L1PA3_dup8328" "L1PA2_dup635" "L1PA3_dup1046"
## [293] "L1PA3_dup9998" "L1PA3_dup7947" "L1PA3_dup5355" "L1PA3_dup3502"
## [297] "L1HS_dup163" "L1HS_dup90" "L1PA2_dup219" "L1PA3_dup907"
## [301] "L1PA3_dup8525" "L1PA2_dup1560" "L1PA3_dup5468" "L1PA3_dup5207"
## [305] "L1HS_dup1393" "L1PA3_dup8571" "L1HS_dup35" "L1PA2_dup1112"
## [309] "L1HS_dup1478" "L1HS_dup1295" "L1HS_dup803" "L1PA3_dup1989"
## [313] "L1PA2_dup4430" "L1PA2_dup4043" "L1PA3_dup6434" "L1PA3_dup1952"
## [317] "L1PA3_dup4708" "L1HS_dup1243" "L1PA2_dup2506" "L1PA3_dup6387"
## [321] "L1PA2_dup1746" "L1PA3_dup247" "L1PA3_dup1528" "L1PA3_dup6929"
## [325] "L1PA2_dup3773" "L1HS_dup1104" "L1PA3_dup7550" "L1PA2_dup741"
## [329] "L1PA3_dup2683" "L1PA3_dup7963" "L1PA2_dup360" "L1HS_dup270"
## [333] "L1PA2_dup4441" "L1PA3_dup3950" "L1PA2_dup358" "L1PA2_dup98"
## [337] "L1HS_dup743" "L1HS_dup811" "L1PA3_dup2954" "L1PA3_dup6730"
## [341] "L1PA2_dup4432" "L1PA3_dup2039" "L1PA3_dup1328" "L1HS_dup579"
## [345] "L1PA3_dup4487" "L1PA3_dup124" "L1PA2_dup2295" "L1HS_dup204"
## [349] "L1PA2_dup472" "L1PA2_dup2004" "L1PA2_dup747" "L1HS_dup87"
## [353] "L1HS_dup1357" "L1PA2_dup2385" "L1PA2_dup2444" "L1PA2_dup4045"
## [357] "L1PA2_dup3766" "L1HS_dup1020" "L1PA2_dup307" "L1HS_dup466"
## [361] "L1PA2_dup3042" "L1PA3_dup4884" "L1HS_dup244" "L1PA2_dup3283"
## [365] "L1PA2_dup4478" "L1PA2_dup2565" "L1PA2_dup196" "L1PA3_dup5745"
## [369] "L1HS_dup1437" "L1PA2_dup2436" "L1PA3_dup7432" "L1PA2_dup1933"
## [373] "L1PA3_dup3880" "L1PA2_dup1078" "L1PA2_dup1023" "L1HS_dup1514"
## [377] "L1PA3_dup2662" "L1PA3_dup4391" "L1PA3_dup7840" "L1PA2_dup413"
## [381] "L1PA3_dup3300" "L1HS_dup1077" "L1PA3_dup8310" "L1PA2_dup1978"
## [385] "L1PA2_dup3118" "L1PA2_dup4522" "L1HS_dup948" "L1PA3_dup4603"
## [389] "L1PA3_dup1554" "L1PA3_dup4259" "L1HS_dup1342" "L1HS_dup879"
## [393] "L1PA3_dup3684" "L1PA3_dup7792" "L1PA2_dup1177" "L1PA3_dup4596"
## [397] "L1PA2_dup326" "L1PA2_dup2271" "L1PA3_dup4122" "L1PA2_dup4378"
## [401] "L1PA2_dup589" "L1PA3_dup3959" "L1HS_dup62" "L1PA2_dup3003"
## [405] "L1PA3_dup5418" "L1PA2_dup4776" "L1PA2_dup1476" "L1PA2_dup3930"
## [409] "L1HS_dup907" "L1PA2_dup3426" "L1PA3_dup1279" "L1PA3_dup5866"
## [413] "L1PA3_dup1027" "L1PA2_dup4618" "L1HS_dup1284" "L1PA2_dup514"
## [417] "L1PA3_dup1463" "L1PA2_dup4335" "L1PA2_dup1248" "L1PA3_dup4687"
## [421] "L1PA3_dup5544" "L1PA2_dup383" "L1PA2_dup4528" "L1HS_dup1005"
## [425] "L1PA2_dup382" "L1HS_dup800" "L1HS_dup1576" "L1PA2_dup2988"
## [429] "L1HS_dup831" "L1PA2_dup365" "L1PA2_dup1049" "L1PA2_dup2127"
## [433] "L1PA3_dup1114" "L1PA2_dup1805" "L1PA3_dup2755" "L1PA3_dup8313"
## [437] "L1PA2_dup1375" "L1PA2_dup1760" "L1PA3_dup1550" "L1PA2_dup3629"
## [441] "L1PA2_dup726" "L1PA2_dup2168" "L1PA3_dup4408" "L1PA3_dup6160"
## [445] "L1PA3_dup8891" "L1PA3_dup7893" "L1PA2_dup2537" "L1PA2_dup2577"
## [449] "L1PA3_dup3323" "L1PA2_dup4389" "L1PA2_dup4226" "L1PA2_dup530"
## [453] "L1HS_dup143" "L1HS_dup1473" "L1PA2_dup1653" "L1PA2_dup3881"
## [457] "L1PA3_dup5540" "L1PA2_dup2089" "L1PA3_dup6584" "L1PA3_dup6112"
## [461] "L1PA2_dup2729" "L1HS_dup1501" "L1PA3_dup9702" "L1PA3_dup4349"
## [465] "L1PA3_dup840" "L1PA3_dup5927" "L1PA2_dup3160" "L1PA2_dup4454"
## [469] "L1PA3_dup5358" "L1PA3_dup3291" "L1PA2_dup2282" "L1PA3_dup345"
## [473] "L1PA2_dup3776" "L1PA3_dup8896" "L1HS_dup225" "L1PA2_dup3439"
## [477] "L1PA3_dup6871" "L1PA3_dup3307" "L1PA3_dup4393" "L1PA3_dup1647"
## [481] "L1PA2_dup1058" "L1HS_dup622" "L1PA3_dup5238" "L1PA3_dup1026"
## [485] "L1PA2_dup3622" "L1PA2_dup4612" "L1PA3_dup1269" "L1PA3_dup1337"
## [489] "L1PA2_dup732" "L1PA3_dup6523" "L1HS_dup1491" "L1PA3_dup5594"
## [493] "L1PA2_dup2876" "L1PA2_dup2430" "L1PA2_dup3445" "L1PA2_dup678"
## [497] "L1HS_dup802" "L1PA3_dup7316" "L1PA3_dup638" "L1PA2_dup2581"
## [501] "L1HS_dup600" "L1PA3_dup9255" "L1PA3_dup10043" "L1PA3_dup5886"
## [505] "L1PA3_dup10072" "L1PA3_dup3005" "L1PA3_dup1943" "L1PA2_dup4611"
## [509] "L1PA3_dup1727" "L1PA3_dup9866" "L1PA3_dup5057" "L1PA2_dup1418"
## [513] "L1PA3_dup9202" "L1PA3_dup7288" "L1PA2_dup4688" "L1PA2_dup4201"
## [517] "L1PA3_dup3404" "L1PA3_dup9722" "L1PA2_dup1463" "L1PA3_dup5825"
asap_heatmap_snRNA(region = c("AMY"),
tes = data_TE_annotation[which(data_TE_annotation$type == "L1"),"TE_id"],
return_df = F,
breaks = seq(0,15,length.out = 52),
data = TE_data,
group_cols = c("celltype"),
index_row_reorder = c(L1s_sorted_amy),
order_cols_groups = order_cols_celltype,
title = "AMY L1s: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
annotation_cols = annotation_cols)

## $heatmap
##
## $order_cols
## [1] "DA805_ASAP56_ctrl_NP19-37_AMY_0" "AA_ASAP115_PD_NP21-208_AMY_0"
## [3] "AA_ASAP110_ctrl_NP16-119_AMY_0" "DA474_ASAP24_PD_NP16-25_AMY_0"
## [5] "DA811_ASAP18_PD_NP16-140_AMY_0" "DA780_ASAP37_PD_NP19-16_AMY_0"
## [7] "DA793_ASAP53_ctrl_NP19-36_AMY_0" "DA778_ASAP31_PD_NP18-117_AMY_0"
## [9] "DA791_ASAP50_ctrl_NP18-159_AMY_0" "DA783_ASAP45_PD_NP19-255_AMY_0"
## [11] "DA802_ASAP40_PD_NP19-23_AMY_0" "AA_ASAP114_PD_NP21-57_AMY_0"
## [13] "AA_ASAP126_PD_NP19-137_AMY_1" "AA_ASAP128_PD_NP21-04_AMY_1"
## [15] "AA_ASAP131_PD_NP23-21_AMY_1" "AA_ASAP121_PD_NP17-232_AMY_1"
## [17] "DA474_ASAP24_PD_NP16-25_AMY_1" "AA_ASAP110_ctrl_NP16-119_AMY_1"
## [19] "AA_ASAP115_PD_NP21-208_AMY_1" "DA512_ASAP60_ctrl_NP19-45_AMY_1"
## [21] "DA805_ASAP56_ctrl_NP19-37_AMY_1" "AA_ASAP113_ctrl_NP18-148_AMY_1"
## [23] "AA_ASAP114_PD_NP21-57_AMY_1" "AA_ASAP119_PD_NP22-55_AMY_1"
## [25] "AA_ASAP123_ctrl_NP19-218_AMY_1" "AA_ASAP124_ctrl_NP22-37_AMY_1"
## [27] "AA_ASAP109_PD_NP21-217_AMY_1" "DA791_ASAP50_ctrl_NP18-159_AMY_1"
## [29] "DA778_ASAP31_PD_NP18-117_AMY_1" "DA793_ASAP53_ctrl_NP19-36_AMY_1"
## [31] "DA802_ASAP40_PD_NP19-23_AMY_1" "DA801_ASAP53_ctrl_NP19-36_AMY_1"
## [33] "DA783_ASAP45_PD_NP19-255_AMY_1" "DA780_ASAP37_PD_NP19-16_AMY_1"
## [35] "DA811_ASAP18_PD_NP16-140_AMY_1" "ASAP122_PD_NP19-91_AMY_2"
## [37] "AA_ASAP109_PD_NP21-217_AMY_2" "AA_ASAP119_PD_NP22-55_AMY_2"
## [39] "AA_ASAP126_PD_NP19-137_AMY_2" "AA_ASAP131_PD_NP23-21_AMY_2"
## [41] "DA814_ASAP35_PD_NP18-304_AMY_2" "AA_ASAP120_PD_NP16-285_AMY_2"
## [43] "AA_ASAP128_PD_NP21-04_AMY_2" "DA783_ASAP45_PD_NP19-255_AMY_2"
## [45] "AA_ASAP115_PD_NP21-208_AMY_2" "DA512_ASAP60_ctrl_NP19-45_AMY_2"
## [47] "DA807_ASAP29_PD_NP17-191_AMY_2" "DA474_ASAP24_PD_NP16-25_AMY_2"
## [49] "DA805_ASAP56_ctrl_NP19-37_AMY_2" "DA811_ASAP18_PD_NP16-140_AMY_2"
## [51] "AA_ASAP124_ctrl_NP22-37_AMY_2" "AA_ASAP121_PD_NP17-232_AMY_2"
## [53] "AA_ASAP112_ctrl_NP16-293_AMY_2" "DA780_ASAP37_PD_NP19-16_AMY_2"
## [55] "AA_ASAP123_ctrl_NP19-218_AMY_2" "AA_ASAP114_PD_NP21-57_AMY_2"
## [57] "AA_ASAP110_ctrl_NP16-119_AMY_2" "AA_ASAP113_ctrl_NP18-148_AMY_2"
## [59] "DA791_ASAP50_ctrl_NP18-159_AMY_2" "DA802_ASAP40_PD_NP19-23_AMY_2"
## [61] "DA778_ASAP31_PD_NP18-117_AMY_2" "DA793_ASAP53_ctrl_NP19-36_AMY_2"
## [63] "DA801_ASAP53_ctrl_NP19-36_AMY_2" "DA780_ASAP37_PD_NP19-16_AMY_3"
## [65] "DA791_ASAP50_ctrl_NP18-159_AMY_3" "DA778_ASAP31_PD_NP18-117_AMY_3"
## [67] "DA803_ASAP48_ctrl_NP17-256_AMY_3" "AA_ASAP131_PD_NP23-21_AMY_3"
## [69] "AA_ASAP111_ctrl_NP16-284_AMY_3" "AA_ASAP115_PD_NP21-208_AMY_3"
## [71] "AA_ASAP112_ctrl_NP16-293_AMY_3" "AA_ASAP120_PD_NP16-285_AMY_3"
## [73] "ASAP122_PD_NP19-91_AMY_3" "DA802_ASAP40_PD_NP19-23_AMY_3"
## [75] "DA811_ASAP18_PD_NP16-140_AMY_3" "AA_ASAP119_PD_NP22-55_AMY_3"
## [77] "DA807_ASAP29_PD_NP17-191_AMY_3" "DA805_ASAP56_ctrl_NP19-37_AMY_3"
## [79] "DA474_ASAP24_PD_NP16-25_AMY_3" "DA793_ASAP53_ctrl_NP19-36_AMY_3"
## [81] "DA801_ASAP53_ctrl_NP19-36_AMY_3" "AA_ASAP123_ctrl_NP19-218_AMY_3"
## [83] "AA_ASAP128_PD_NP21-04_AMY_3" "AA_ASAP110_ctrl_NP16-119_AMY_3"
## [85] "AA_ASAP114_PD_NP21-57_AMY_3" "DA512_ASAP60_ctrl_NP19-45_AMY_3"
## [87] "AA_ASAP113_ctrl_NP18-148_AMY_3" "AA_ASAP124_ctrl_NP22-37_AMY_3"
## [89] "DA783_ASAP45_PD_NP19-255_AMY_3" "AA_ASAP121_PD_NP17-232_AMY_3"
## [91] "AA_ASAP109_PD_NP21-217_AMY_3" "DA800_ASAP20_PD_NP16-160_AMY_5"
## [93] "AA_ASAP128_PD_NP21-04_AMY_5" "AA_ASAP131_PD_NP23-21_AMY_5"
## [95] "DA783_ASAP45_PD_NP19-255_AMY_5" "AA_ASAP110_ctrl_NP16-119_AMY_5"
## [97] "AA_ASAP115_PD_NP21-208_AMY_5" "AA_ASAP126_PD_NP19-137_AMY_5"
## [99] "DA512_ASAP60_ctrl_NP19-45_AMY_5" "DA778_ASAP31_PD_NP18-117_AMY_5"
## [101] "DA802_ASAP40_PD_NP19-23_AMY_5" "DA803_ASAP48_ctrl_NP17-256_AMY_5"
## [103] "AA_ASAP120_PD_NP16-285_AMY_5" "DA779_ASAP33_PD_NP18-287_AMY_5"
## [105] "DA815_ASAP37_PD_NP19-16_AMY_5" "DA814_ASAP35_PD_NP18-304_AMY_5"
## [107] "AA_ASAP121_PD_NP17-232_AMY_5" "DA811_ASAP18_PD_NP16-140_AMY_5"
## [109] "DA807_ASAP29_PD_NP17-191_AMY_5" "DA780_ASAP37_PD_NP19-16_AMY_5"
## [111] "DA791_ASAP50_ctrl_NP18-159_AMY_5" "AA_ASAP123_ctrl_NP19-218_AMY_5"
## [113] "AA_ASAP119_PD_NP22-55_AMY_5" "DA805_ASAP56_ctrl_NP19-37_AMY_5"
## [115] "DA474_ASAP24_PD_NP16-25_AMY_5" "AA_ASAP114_PD_NP21-57_AMY_5"
## [117] "AA_ASAP113_ctrl_NP18-148_AMY_5" "ASAP122_PD_NP19-91_AMY_5"
## [119] "AA_ASAP109_PD_NP21-217_AMY_5" "AA_ASAP124_ctrl_NP22-37_AMY_5"
## [121] "AA_ASAP112_ctrl_NP16-293_AMY_5" "DA793_ASAP53_ctrl_NP19-36_AMY_5"
## [123] "DA801_ASAP53_ctrl_NP19-36_AMY_5" "AA_ASAP131_PD_NP23-21_AMY_4"
## [125] "DA512_ASAP60_ctrl_NP19-45_AMY_4" "AA_ASAP126_PD_NP19-137_AMY_4"
## [127] "AA_ASAP112_ctrl_NP16-293_AMY_4" "AA_ASAP115_PD_NP21-208_AMY_4"
## [129] "DA802_ASAP40_PD_NP19-23_AMY_4" "DA811_ASAP18_PD_NP16-140_AMY_4"
## [131] "DA801_ASAP53_ctrl_NP19-36_AMY_4" "AA_ASAP110_ctrl_NP16-119_AMY_4"
## [133] "DA793_ASAP53_ctrl_NP19-36_AMY_4" "DA805_ASAP56_ctrl_NP19-37_AMY_4"
## [135] "DA474_ASAP24_PD_NP16-25_AMY_4" "DA807_ASAP29_PD_NP17-191_AMY_4"
## [137] "AA_ASAP123_ctrl_NP19-218_AMY_4" "AA_ASAP114_PD_NP21-57_AMY_4"
## [139] "AA_ASAP113_ctrl_NP18-148_AMY_4" "DA783_ASAP45_PD_NP19-255_AMY_4"
## [141] "AA_ASAP119_PD_NP22-55_AMY_4" "DA791_ASAP50_ctrl_NP18-159_AMY_4"
## [143] "DA778_ASAP31_PD_NP18-117_AMY_4" "AA_ASAP123_ctrl_NP19-218_AMY_6"
##
## $order_rows
## [1] "L1PA2_dup1230" "L1PA2_dup848" "L1PA2_dup791" "L1HS_dup1462"
## [5] "L1PA3_dup398" "L1PA2_dup4403" "L1PA2_dup585" "L1PA2_dup234"
## [9] "L1HS_dup337" "L1PA3_dup1010" "L1PA3_dup10686" "L1PA2_dup922"
## [13] "L1PA3_dup2744" "L1PA2_dup513" "L1HS_dup124" "L1PA2_dup378"
## [17] "L1PA3_dup4994" "L1PA3_dup6385" "L1HS_dup1324" "L1PA3_dup2204"
## [21] "L1HS_dup455" "L1PA2_dup663" "L1PA3_dup8903" "L1PA3_dup10285"
## [25] "L1PA2_dup2245" "L1PA2_dup4651" "L1PA3_dup8173" "L1PA3_dup2557"
## [29] "L1PA2_dup1462" "L1PA3_dup1651" "L1PA2_dup1298" "L1PA2_dup526"
## [33] "L1PA3_dup4492" "L1PA2_dup949" "L1PA3_dup2413" "L1PA3_dup3102"
## [37] "L1PA3_dup1" "L1PA3_dup2919" "L1PA2_dup3736" "L1PA3_dup8522"
## [41] "L1PA3_dup10297" "L1PA3_dup2593" "L1PA3_dup761" "L1PA2_dup1621"
## [45] "L1PA3_dup8663" "L1PA3_dup9946" "L1PA2_dup927" "L1PA2_dup4074"
## [49] "L1HS_dup916" "L1PA3_dup7864" "L1PA3_dup1756" "L1PA3_dup4118"
## [53] "L1PA2_dup3607" "L1PA3_dup358" "L1PA3_dup8872" "L1PA2_dup559"
## [57] "L1HS_dup1342" "L1PA3_dup4709" "L1PA3_dup9021" "L1PA2_dup37"
## [61] "L1PA2_dup109" "L1PA3_dup2517" "L1PA3_dup9095" "L1PA3_dup872"
## [65] "L1PA2_dup2680" "L1PA2_dup39" "L1PA2_dup3484" "L1PA3_dup2760"
## [69] "L1PA3_dup10119" "L1PA3_dup400" "L1PA3_dup1264" "L1PA2_dup2720"
## [73] "L1PA2_dup2504" "L1PA3_dup1710" "L1HS_dup1286" "L1PA2_dup2909"
## [77] "L1HS_dup649" "L1PA3_dup3757" "L1PA2_dup1953" "L1HS_dup138"
## [81] "L1PA2_dup3664" "L1PA3_dup6036" "L1PA2_dup737" "L1PA2_dup4620"
## [85] "L1PA3_dup373" "L1PA3_dup4891" "L1PA2_dup727" "L1PA3_dup8420"
## [89] "L1PA3_dup9430" "L1HS_dup879" "L1PA3_dup3758" "L1PA2_dup2180"
## [93] "L1PA3_dup5337" "L1PA2_dup2289" "L1PA2_dup675" "L1PA3_dup3168"
## [97] "L1PA3_dup10740" "L1PA3_dup7821" "L1PA3_dup4888" "L1PA2_dup2091"
## [101] "L1PA3_dup6002" "L1PA2_dup3136" "L1PA2_dup200" "L1PA2_dup4936"
## [105] "L1PA2_dup3579" "L1HS_dup444" "L1PA3_dup561" "L1PA3_dup8506"
## [109] "L1PA3_dup1770" "L1PA2_dup3425" "L1PA3_dup4277" "L1PA3_dup5928"
## [113] "L1PA3_dup978" "L1PA2_dup2969" "L1PA3_dup9702" "L1PA2_dup3405"
## [117] "L1PA3_dup1547" "L1PA2_dup1490" "L1PA3_dup4603" "L1PA3_dup3863"
## [121] "L1PA2_dup3771" "L1PA3_dup4885" "L1PA3_dup6147" "L1PA3_dup4487"
## [125] "L1PA3_dup2721" "L1PA2_dup410" "L1PA3_dup2551" "L1PA3_dup5514"
## [129] "L1PA2_dup2408" "L1PA2_dup2860" "L1PA2_dup1177" "L1HS_dup240"
## [133] "L1PA3_dup529" "L1PA2_dup130" "L1PA2_dup3589" "L1PA3_dup7470"
## [137] "L1PA2_dup4838" "L1PA2_dup221" "L1HS_dup1357" "L1PA3_dup9280"
## [141] "L1PA3_dup10525" "L1PA3_dup3586" "L1PA2_dup3805" "L1PA3_dup2662"
## [145] "L1PA3_dup8891" "L1PA3_dup3300" "L1PA3_dup527" "L1PA3_dup1428"
## [149] "L1PA3_dup7550" "L1PA3_dup9473" "L1PA2_dup1272" "L1PA3_dup2272"
## [153] "L1PA3_dup6884" "L1PA3_dup9256" "L1PA3_dup748" "L1PA3_dup5121"
## [157] "L1HS_dup449" "L1PA2_dup1379" "L1HS_dup1014" "L1PA2_dup4548"
## [161] "L1HS_dup788" "L1PA2_dup2004" "L1PA3_dup6457" "L1PA2_dup3531"
## [165] "L1PA2_dup4421" "L1HS_dup1536" "L1PA2_dup423" "L1HS_dup596"
## [169] "L1PA3_dup8525" "L1PA2_dup1752" "L1PA2_dup2791" "L1PA3_dup7951"
## [173] "L1PA3_dup4884" "L1PA2_dup759" "L1PA2_dup595" "L1HS_dup111"
## [177] "L1PA2_dup1749" "L1PA3_dup7605" "L1PA2_dup684" "L1HS_dup632"
## [181] "L1PA3_dup1311" "L1PA3_dup5680" "L1PA2_dup3283" "L1PA3_dup3941"
## [185] "L1PA2_dup2047" "L1HS_dup800" "L1PA2_dup4053" "L1PA3_dup3306"
## [189] "L1PA3_dup8571" "L1PA2_dup3773" "L1PA2_dup2496" "L1PA3_dup8007"
## [193] "L1PA3_dup4668" "L1PA3_dup8520" "L1PA3_dup6317" "L1HS_dup191"
## [197] "L1PA3_dup9840" "L1HS_dup35" "L1PA3_dup247" "L1PA3_dup10011"
## [201] "L1HS_dup155" "L1PA2_dup1778" "L1PA3_dup5594" "L1PA3_dup6008"
## [205] "L1PA3_dup2683" "L1PA2_dup142" "L1PA3_dup1937" "L1HS_dup995"
## [209] "L1PA2_dup2385" "L1PA3_dup1800" "L1PA3_dup6692" "L1HS_dup1330"
## [213] "L1PA2_dup2863" "L1PA3_dup1554" "L1PA2_dup2164" "L1PA3_dup3763"
## [217] "L1PA2_dup4454" "L1PA3_dup3507" "L1PA2_dup16" "L1PA3_dup1723"
## [221] "L1HS_dup429" "L1PA3_dup8310" "L1HS_dup1005" "L1HS_dup1393"
## [225] "L1PA2_dup382" "L1PA2_dup1760" "L1PA2_dup3292" "L1PA3_dup6573"
## [229] "L1PA3_dup2643" "L1PA2_dup2729" "L1PA3_dup9373" "L1PA2_dup4441"
## [233] "L1PA2_dup2988" "L1PA3_dup6434" "L1PA2_dup1746" "L1PA3_dup6929"
## [237] "L1PA2_dup2254" "L1PA2_dup2155" "L1PA3_dup10096" "L1PA3_dup6550"
## [241] "L1PA2_dup4762" "L1PA2_dup1049" "L1PA3_dup5510" "L1PA2_dup1112"
## [245] "L1PA2_dup4612" "L1PA2_dup4686" "L1HS_dup204" "L1PA3_dup1988"
## [249] "L1PA2_dup678" "L1PA2_dup935" "L1PA3_dup3954" "L1PA2_dup4335"
## [253] "L1HS_dup225" "L1HS_dup514" "L1PA2_dup635" "L1HS_dup1019"
## [257] "L1PA2_dup3437" "L1PA2_dup2343" "L1PA3_dup4401" "L1PA2_dup1933"
## [261] "L1HS_dup743" "L1PA3_dup2954" "L1PA3_dup7237" "L1PA2_dup1331"
## [265] "L1HS_dup379" "L1PA3_dup165" "L1PA3_dup1550" "L1PA2_dup326"
## [269] "L1PA2_dup4528" "L1HS_dup948" "L1PA2_dup662" "L1PA3_dup907"
## [273] "L1PA3_dup9734" "L1HS_dup679" "L1PA2_dup71" "L1PA3_dup2039"
## [277] "L1PA2_dup4596" "L1PA3_dup2620" "L1PA3_dup4408" "L1PA3_dup7963"
## [281] "L1PA2_dup4045" "L1PA2_dup4775" "L1PA3_dup5866" "L1PA3_dup3484"
## [285] "L1PA3_dup4804" "L1PA3_dup4393" "L1PA3_dup5534" "L1PA2_dup4030"
## [289] "L1PA3_dup7862" "L1PA3_dup7472" "L1HS_dup1104" "L1PA3_dup10344"
## [293] "L1PA2_dup365" "L1HS_dup579" "L1PA3_dup3502" "L1PA2_dup4522"
## [297] "L1PA2_dup2537" "L1PA3_dup6436" "L1HS_dup1514" "L1PA2_dup4714"
## [301] "L1PA3_dup2393" "L1PA2_dup1560" "L1HS_dup62" "L1PA3_dup3729"
## [305] "L1HS_dup1182" "L1PA2_dup1770" "L1PA2_dup1653" "L1PA3_dup5544"
## [309] "L1PA2_dup2282" "L1PA2_dup3118" "L1PA3_dup5745" "L1HS_dup802"
## [313] "L1PA2_dup4776" "L1HS_dup622" "L1PA3_dup3291" "L1HS_dup1473"
## [317] "L1HS_dup1478" "L1PA3_dup6347" "L1PA3_dup7288" "L1PA3_dup10176"
## [321] "L1PA3_dup1463" "L1HS_dup163" "L1HS_dup811" "L1PA3_dup9998"
## [325] "L1PA3_dup7637" "L1PA3_dup9722" "L1PA2_dup413" "L1HS_dup1339"
## [329] "L1HS_dup466" "L1PA2_dup2127" "L1HS_dup370" "L1HS_dup787"
## [333] "L1PA3_dup3509" "L1PA2_dup1398" "L1PA3_dup8896" "L1PA3_dup3968"
## [337] "L1PA3_dup1114" "L1PA2_dup805" "L1PA2_dup747" "L1PA3_dup3404"
## [341] "L1PA3_dup2357" "L1PA3_dup6387" "L1PA2_dup472" "L1PA3_dup4391"
## [345] "L1PA3_dup3307" "L1PA2_dup307" "L1PA2_dup2436" "L1HS_dup803"
## [349] "L1PA3_dup5106" "L1PA3_dup7947" "L1PA3_dup3323" "L1PA2_dup514"
## [353] "L1HS_dup270" "L1HS_dup1576" "L1PA2_dup4478" "L1PA3_dup2389"
## [357] "L1PA3_dup4122" "L1PA2_dup994" "L1PA3_dup8313" "L1PA2_dup3881"
## [361] "L1PA2_dup2444" "L1HS_dup244" "L1PA2_dup2089" "L1PA3_dup5468"
## [365] "L1HS_dup1077" "L1PA2_dup1023" "L1PA3_dup2755" "L1PA3_dup3880"
## [369] "L1PA3_dup5355" "L1PA2_dup1050" "L1HS_dup405" "L1PA3_dup6730"
## [373] "L1PA2_dup1248" "L1HS_dup831" "L1PA2_dup3615" "L1PA2_dup3622"
## [377] "L1PA3_dup4259" "L1HS_dup1437" "L1PA3_dup683" "L1PA3_dup4708"
## [381] "L1PA2_dup2581" "L1PA3_dup8117" "L1PA2_dup4618" "L1PA3_dup7840"
## [385] "L1PA2_dup4430" "L1PA3_dup124" "L1PA2_dup4440" "L1HS_dup376"
## [389] "L1PA3_dup128" "L1PA3_dup8328" "L1PA2_dup2506" "L1PA3_dup4688"
## [393] "L1PA2_dup1426" "L1PA2_dup3042" "L1PA2_dup4389" "L1HS_dup1020"
## [397] "L1PA2_dup1992" "L1PA2_dup4262" "L1PA3_dup5238" "L1PA3_dup5886"
## [401] "L1PA3_dup6112" "L1PA3_dup7893" "L1PA3_dup5927" "L1PA3_dup6160"
## [405] "L1PA2_dup4652" "L1PA3_dup6966" "L1PA2_dup1805" "L1PA2_dup629"
## [409] "L1PA2_dup741" "L1PA2_dup2577" "L1PA3_dup7432" "L1PA2_dup4639"
## [413] "L1PA2_dup196" "L1PA3_dup10072" "L1PA3_dup10043" "L1PA3_dup840"
## [417] "L1PA2_dup4196" "L1PA2_dup530" "L1PA2_dup2295" "L1PA3_dup5207"
## [421] "L1PA3_dup3684" "L1PA2_dup798" "L1PA2_dup2271" "L1PA2_dup4791"
## [425] "L1HS_dup1284" "L1PA2_dup2876" "L1PA2_dup3003" "L1PA3_dup1328"
## [429] "L1PA2_dup726" "L1PA2_dup3742" "L1PA3_dup1528" "L1PA2_dup4432"
## [433] "L1PA2_dup4901" "L1PA3_dup1989" "L1PA2_dup1463" "L1PA2_dup4043"
## [437] "L1HS_dup87" "L1PA2_dup1978" "L1PA2_dup3445" "L1HS_dup90"
## [441] "L1PA2_dup4237" "L1PA2_dup4611" "L1HS_dup1616" "L1PA3_dup9866"
## [445] "L1PA3_dup3153" "L1HS_dup1501" "L1PA2_dup219" "L1PA3_dup6584"
## [449] "L1PA3_dup4349" "L1PA2_dup4367" "L1PA3_dup1269" "L1PA3_dup3959"
## [453] "L1PA2_dup4309" "L1PA2_dup3503" "L1PA2_dup358" "L1PA3_dup4902"
## [457] "L1HS_dup143" "L1PA2_dup4905" "L1PA3_dup5358" "L1PA3_dup5047"
## [461] "L1PA3_dup5363" "L1PA3_dup1046" "L1PA2_dup360" "L1PA2_dup1476"
## [465] "L1PA3_dup1027" "L1PA2_dup3426" "L1HS_dup1243" "L1PA2_dup4378"
## [469] "L1PA3_dup9856" "L1PA3_dup1026" "L1PA3_dup5825" "L1PA3_dup638"
## [473] "L1PA3_dup7792" "L1PA3_dup4596" "L1PA3_dup1952" "L1PA2_dup3160"
## [477] "L1PA3_dup345" "L1PA2_dup1375" "L1PA2_dup3439" "L1PA3_dup10531"
## [481] "L1PA3_dup9255" "L1PA2_dup2168" "L1PA3_dup9202" "L1HS_dup907"
## [485] "L1PA3_dup1727" "L1PA2_dup2565" "L1HS_dup1491" "L1PA3_dup1279"
## [489] "L1PA2_dup383" "L1PA2_dup3930" "L1PA2_dup1058" "L1PA3_dup3005"
## [493] "L1PA2_dup4201" "L1PA3_dup5418" "L1PA2_dup2430" "L1PA3_dup7316"
## [497] "L1PA2_dup3766" "L1PA3_dup5540" "L1PA2_dup589" "L1PA3_dup1647"
## [501] "L1PA2_dup3776" "L1PA2_dup4713" "L1PA2_dup3629" "L1PA2_dup732"
## [505] "L1PA2_dup1968" "L1PA3_dup4687" "L1PA2_dup1418" "L1PA3_dup3950"
## [509] "L1PA2_dup98" "L1PA3_dup1337" "L1HS_dup600" "L1PA3_dup5057"
## [513] "L1PA3_dup6871" "L1HS_dup1295" "L1PA2_dup1078" "L1PA2_dup4226"
## [517] "L1PA3_dup1943" "L1PA3_dup6523" "L1PA2_dup2261" "L1PA2_dup4688"
asap_heatmap_snRNA(region = c("SN"),
tes = data_TE_annotation[which(data_TE_annotation$type == "L1"),"TE_id"],
return_df = F,
breaks = seq(0,15,length.out = 52),
data = TE_data,
group_cols = c("celltype"),
index_row_reorder = c(L1s_sorted_sn),
order_cols_groups = order_cols_celltype,
title = "SN L1s: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
annotation_cols = annotation_cols)

## $heatmap
##
## $order_cols
## [1] "AA_ASAP129_ctrl_NP22-37_SN_1" "AA_ASAP118_PD_NP22-55_SN_1"
## [3] "DA792_ASAP51_ctrl_NP19-36_SN_1" "AA_ASAP137_PD_NP23-21_SN_1"
## [5] "DA487_ASAP8_ctrl_PT231_SN_1" "DA479_ASAP7_ctrl_NP16-21_SN_2"
## [7] "DA487_ASAP8_ctrl_PT231_SN_2" "AA_ASAP127_ctrl_NP19-218_SN_2"
## [9] "AA_ASAP108_ctrl_NP18-148_SN_2" "DA433_ASAP5_ctrl_NP16-161_SN_2"
## [11] "AA_ASAP99_ctrl_NP16-284_SN_2" "DA431_ASAP4_PD_P74_SN_2"
## [13] "DA782_ASAP41_PD_NP19-108_SN_2" "AA_ASAP129_ctrl_NP22-37_SN_2"
## [15] "AA_ASAP118_PD_NP22-55_SN_2" "DA784_ASAP46_ctrl_NP17-256_SN_2"
## [17] "DA475_ASAP2_PD_NP16-25_SN_2" "AA_ASAP133_PD_NP17-232_SN_2"
## [19] "MJ_ASAP6_ctrl_NP16-164_SN_2" "AA_ASAP137_PD_NP23-21_SN_2"
## [21] "DA792_ASAP51_ctrl_NP19-36_SN_2" "AA_ASAP135_PD_NP19-137_SN_2"
## [23] "DA794_ASAP54_ctrl_NP19-37_SN_2" "AA_ASAP101_PD_NP21-57_SN_2"
## [25] "DA489_ASAP3_PD_P73_SN_2" "AA_ASAP103_PD_NP21-217_SN_2"
## [27] "AA_ASAP102_PD_NP21-208_SN_2" "DA429_ASAP1_PD_NP16-162_SN_2"
## [29] "DA473_ASAP38_PD_NP19-23_SN_2" "AA_ASAP105_ctrl_NP16-293_SN_2"
## [31] "DA511_ASAP21_PD_NP16-269_SN_2" "AA_ASAP134_PD_NP19-91_SN_2"
## [33] "AA_ASAP104_ctrl_NP16-119_SN_2" "AA_ASAP132_PD_NP16-285_SN_2"
## [35] "DA796_ASAP57_ctrl_NP19-45_SN_2" "MJ_ASAP6_ctrl_NP16-164_SN_3"
## [37] "AA_ASAP129_ctrl_NP22-37_SN_3" "DA489_ASAP3_PD_P73_SN_3"
## [39] "DA475_ASAP2_PD_NP16-25_SN_3" "DA433_ASAP5_ctrl_NP16-161_SN_3"
## [41] "DA479_ASAP7_ctrl_NP16-21_SN_3" "DA431_ASAP4_PD_P74_SN_3"
## [43] "AA_ASAP133_PD_NP17-232_SN_3" "AA_ASAP137_PD_NP23-21_SN_3"
## [45] "AA_ASAP135_PD_NP19-137_SN_3" "AA_ASAP127_ctrl_NP19-218_SN_3"
## [47] "AA_ASAP103_PD_NP21-217_SN_3" "DA511_ASAP21_PD_NP16-269_SN_3"
## [49] "AA_ASAP101_PD_NP21-57_SN_3" "AA_ASAP102_PD_NP21-208_SN_3"
## [51] "AA_ASAP136_PD_NP21-04_SN_3" "AA_ASAP132_PD_NP16-285_SN_3"
## [53] "AA_ASAP99_ctrl_NP16-284_SN_3" "AA_ASAP104_ctrl_NP16-119_SN_3"
## [55] "DA782_ASAP41_PD_NP19-108_SN_3" "AA_ASAP134_PD_NP19-91_SN_3"
## [57] "AA_ASAP118_PD_NP22-55_SN_3" "DA796_ASAP57_ctrl_NP19-45_SN_3"
## [59] "DA784_ASAP46_ctrl_NP17-256_SN_3" "DA487_ASAP8_ctrl_PT231_SN_3"
## [61] "DA473_ASAP38_PD_NP19-23_SN_3" "AA_ASAP105_ctrl_NP16-293_SN_3"
## [63] "AA_ASAP108_ctrl_NP18-148_SN_3" "DA429_ASAP1_PD_NP16-162_SN_3"
## [65] "DA794_ASAP54_ctrl_NP19-37_SN_3" "DA792_ASAP51_ctrl_NP19-36_SN_3"
## [67] "MJ_ASAP6_ctrl_NP16-164_SN_5" "AA_ASAP129_ctrl_NP22-37_SN_5"
## [69] "DA489_ASAP3_PD_P73_SN_5" "AA_ASAP136_PD_NP21-04_SN_5"
## [71] "AA_ASAP132_PD_NP16-285_SN_5" "DA784_ASAP46_ctrl_NP17-256_SN_5"
## [73] "DA487_ASAP8_ctrl_PT231_SN_5" "AA_ASAP105_ctrl_NP16-293_SN_5"
## [75] "AA_ASAP118_PD_NP22-55_SN_5" "AA_ASAP137_PD_NP23-21_SN_5"
## [77] "AA_ASAP127_ctrl_NP19-218_SN_5" "DA511_ASAP21_PD_NP16-269_SN_5"
## [79] "DA475_ASAP2_PD_NP16-25_SN_5" "AA_ASAP135_PD_NP19-137_SN_5"
## [81] "DA473_ASAP38_PD_NP19-23_SN_5" "DA431_ASAP4_PD_P74_SN_5"
## [83] "DA433_ASAP5_ctrl_NP16-161_SN_5" "AA_ASAP101_PD_NP21-57_SN_5"
## [85] "AA_ASAP103_PD_NP21-217_SN_5" "AA_ASAP104_ctrl_NP16-119_SN_5"
## [87] "AA_ASAP108_ctrl_NP18-148_SN_5" "DA794_ASAP54_ctrl_NP19-37_SN_5"
## [89] "AA_ASAP102_PD_NP21-208_SN_5" "AA_ASAP99_ctrl_NP16-284_SN_5"
## [91] "DA429_ASAP1_PD_NP16-162_SN_5" "DA479_ASAP7_ctrl_NP16-21_SN_5"
## [93] "AA_ASAP133_PD_NP17-232_SN_5" "AA_ASAP134_PD_NP19-91_SN_5"
## [95] "DA782_ASAP41_PD_NP19-108_SN_5" "DA792_ASAP51_ctrl_NP19-36_SN_5"
## [97] "DA796_ASAP57_ctrl_NP19-45_SN_5" "AA_ASAP134_PD_NP19-91_SN_4"
## [99] "DA431_ASAP4_PD_P74_SN_4" "AA_ASAP129_ctrl_NP22-37_SN_4"
## [101] "DA487_ASAP8_ctrl_PT231_SN_4" "DA433_ASAP5_ctrl_NP16-161_SN_4"
## [103] "DA475_ASAP2_PD_NP16-25_SN_4" "AA_ASAP137_PD_NP23-21_SN_4"
## [105] "DA473_ASAP38_PD_NP19-23_SN_4" "AA_ASAP104_ctrl_NP16-119_SN_4"
## [107] "DA511_ASAP21_PD_NP16-269_SN_4" "DA489_ASAP3_PD_P73_SN_4"
## [109] "AA_ASAP127_ctrl_NP19-218_SN_4" "AA_ASAP101_PD_NP21-57_SN_4"
## [111] "DA792_ASAP51_ctrl_NP19-36_SN_4" "DA794_ASAP54_ctrl_NP19-37_SN_4"
## [113] "AA_ASAP133_PD_NP17-232_SN_4" "AA_ASAP118_PD_NP22-55_SN_4"
## [115] "AA_ASAP103_PD_NP21-217_SN_4" "AA_ASAP135_PD_NP19-137_SN_4"
## [117] "DA782_ASAP41_PD_NP19-108_SN_4" "AA_ASAP102_PD_NP21-208_SN_4"
## [119] "AA_ASAP108_ctrl_NP18-148_SN_4" "MJ_ASAP6_ctrl_NP16-164_SN_4"
## [121] "DA429_ASAP1_PD_NP16-162_SN_4" "AA_ASAP137_PD_NP23-21_SN_6"
## [123] "DA792_ASAP51_ctrl_NP19-36_SN_6" "AA_ASAP133_PD_NP17-232_SN_7"
## [125] "AA_ASAP137_PD_NP23-21_SN_7" "AA_ASAP108_ctrl_NP18-148_SN_7"
##
## $order_rows
## [1] "L1PA2_dup791" "L1PA2_dup1230" "L1PA2_dup848" "L1PA3_dup398"
## [5] "L1PA2_dup4403" "L1HS_dup1462" "L1PA3_dup7864" "L1PA3_dup529"
## [9] "L1PA2_dup234" "L1PA2_dup585" "L1PA3_dup4994" "L1PA2_dup1933"
## [13] "L1HS_dup337" "L1PA2_dup922" "L1PA3_dup10686" "L1PA2_dup513"
## [17] "L1PA3_dup1010" "L1PA2_dup4905" "L1HS_dup455" "L1PA3_dup1651"
## [21] "L1PA3_dup8903" "L1PA3_dup2744" "L1PA2_dup3736" "L1PA3_dup2557"
## [25] "L1PA3_dup358" "L1PA3_dup10285" "L1PA3_dup8872" "L1PA3_dup6385"
## [29] "L1PA2_dup663" "L1PA3_dup1" "L1PA2_dup2720" "L1PA3_dup10297"
## [33] "L1PA3_dup3102" "L1PA3_dup761" "L1PA3_dup3757" "L1PA3_dup10119"
## [37] "L1PA3_dup8522" "L1PA2_dup4548" "L1PA3_dup400" "L1PA2_dup3405"
## [41] "L1PA2_dup559" "L1PA2_dup1462" "L1PA2_dup526" "L1PA2_dup927"
## [45] "L1PA3_dup2413" "L1PA3_dup4709" "L1PA2_dup37" "L1PA3_dup2204"
## [49] "L1PA3_dup8173" "L1PA3_dup872" "L1PA2_dup4651" "L1PA2_dup4309"
## [53] "L1PA2_dup949" "L1PA2_dup39" "L1PA3_dup9256" "L1PA3_dup5358"
## [57] "L1PA2_dup4528" "L1HS_dup1536" "L1PA3_dup9430" "L1PA3_dup1710"
## [61] "L1PA2_dup2245" "L1PA2_dup200" "L1PA2_dup675" "L1PA3_dup3323"
## [65] "L1PA2_dup423" "L1PA3_dup4118" "L1PA2_dup16" "L1PA2_dup378"
## [69] "L1PA3_dup4891" "L1PA3_dup373" "L1PA3_dup2919" "L1PA3_dup10740"
## [73] "L1PA3_dup1756" "L1PA2_dup3607" "L1PA2_dup142" "L1PA3_dup7472"
## [77] "L1PA2_dup1298" "L1PA3_dup8663" "L1PA2_dup3589" "L1PA2_dup4620"
## [81] "L1PA3_dup3758" "L1PA2_dup1379" "L1PA3_dup2517" "L1PA3_dup2760"
## [85] "L1PA3_dup4804" "L1PA3_dup7470" "L1PA2_dup1621" "L1PA2_dup2680"
## [89] "L1PA3_dup6002" "L1HS_dup1576" "L1PA2_dup2289" "L1PA2_dup2565"
## [93] "L1HS_dup1324" "L1PA3_dup6036" "L1PA3_dup8506" "L1PA2_dup3805"
## [97] "L1PA3_dup7862" "L1PA2_dup4030" "L1PA3_dup5928" "L1PA2_dup741"
## [101] "L1PA2_dup3484" "L1PA3_dup4888" "L1PA2_dup3771" "L1HS_dup1182"
## [105] "L1PA2_dup4686" "L1PA2_dup3118" "L1PA3_dup2551" "L1PA2_dup2969"
## [109] "L1PA3_dup9473" "L1PA2_dup1752" "L1HS_dup1330" "L1PA3_dup1800"
## [113] "L1PA2_dup2791" "L1PA3_dup8571" "L1PA2_dup410" "L1PA3_dup9095"
## [117] "L1PA2_dup1778" "L1PA3_dup3168" "L1PA3_dup2393" "L1HS_dup995"
## [121] "L1PA3_dup5121" "L1PA3_dup4885" "L1PA2_dup727" "L1PA2_dup2506"
## [125] "L1PA2_dup2909" "L1HS_dup632" "L1PA3_dup6317" "L1PA2_dup4688"
## [129] "L1PA2_dup221" "L1PA3_dup1547" "L1PA3_dup1311" "L1PA3_dup3586"
## [133] "L1PA2_dup1953" "L1PA3_dup5106" "L1PA3_dup9998" "L1HS_dup800"
## [137] "L1HS_dup514" "L1PA3_dup10525" "L1PA3_dup4487" "L1PA3_dup5680"
## [141] "L1HS_dup240" "L1PA3_dup1937" "L1PA3_dup4277" "L1PA3_dup5514"
## [145] "L1PA3_dup6147" "L1HS_dup879" "L1PA3_dup527" "L1PA2_dup4618"
## [149] "L1PA3_dup2593" "L1HS_dup649" "L1HS_dup1014" "L1PA2_dup3664"
## [153] "L1HS_dup1473" "L1HS_dup376" "L1PA2_dup662" "L1PA2_dup4762"
## [157] "L1PA3_dup8007" "L1PA3_dup5534" "L1PA3_dup1428" "L1PA3_dup9280"
## [161] "L1PA3_dup5337" "L1PA3_dup4687" "L1PA2_dup1490" "L1PA3_dup4492"
## [165] "L1PA2_dup2164" "L1PA3_dup3684" "L1HS_dup191" "L1HS_dup788"
## [169] "L1PA3_dup3307" "L1PA2_dup4440" "L1PA2_dup2343" "L1PA2_dup2860"
## [173] "L1PA3_dup7550" "L1PA3_dup1264" "L1PA3_dup7821" "L1PA3_dup128"
## [177] "L1PA2_dup1749" "L1PA3_dup4401" "L1PA2_dup4074" "L1PA3_dup7963"
## [181] "L1PA3_dup6457" "L1HS_dup1005" "L1PA3_dup4902" "L1PA3_dup9021"
## [185] "L1HS_dup379" "L1PA2_dup737" "L1PA3_dup3968" "L1PA3_dup1723"
## [189] "L1PA2_dup71" "L1PA2_dup130" "L1PA2_dup4936" "L1PA3_dup4884"
## [193] "L1PA2_dup2155" "L1PA2_dup4596" "L1HS_dup444" "L1HS_dup1286"
## [197] "L1PA2_dup2091" "L1PA3_dup978" "L1HS_dup155" "L1PA3_dup2721"
## [201] "L1PA2_dup726" "L1HS_dup124" "L1PA3_dup561" "L1PA2_dup2385"
## [205] "L1PA3_dup9840" "L1HS_dup916" "L1PA2_dup1272" "L1PA2_dup1476"
## [209] "L1PA3_dup907" "L1PA3_dup1989" "L1PA2_dup1770" "L1PA3_dup6692"
## [213] "L1PA2_dup219" "L1PA2_dup935" "L1PA3_dup1554" "L1PA2_dup3136"
## [217] "L1PA2_dup589" "L1PA3_dup6347" "L1PA3_dup3300" "L1PA3_dup8420"
## [221] "L1PA2_dup2180" "L1HS_dup948" "L1PA2_dup2863" "L1PA2_dup1746"
## [225] "L1PA3_dup7951" "L1PA3_dup3306" "L1PA3_dup3502" "L1PA3_dup5745"
## [229] "L1PA2_dup109" "L1PA2_dup595" "L1PA3_dup3763" "L1PA3_dup8525"
## [233] "L1PA3_dup1269" "L1PA2_dup4522" "L1PA3_dup10344" "L1PA2_dup3776"
## [237] "L1HS_dup111" "L1PA2_dup3437" "L1PA2_dup994" "L1PA2_dup382"
## [241] "L1HS_dup1393" "L1PA2_dup1398" "L1PA3_dup2357" "L1PA3_dup6008"
## [245] "L1PA3_dup6550" "L1PA3_dup5544" "L1PA2_dup1805" "L1PA2_dup3531"
## [249] "L1PA3_dup124" "L1PA3_dup3941" "L1PA3_dup2954" "L1PA3_dup4668"
## [253] "L1PA2_dup3292" "L1HS_dup449" "L1PA2_dup4196" "L1PA3_dup1528"
## [257] "L1PA2_dup2168" "L1PA3_dup4708" "L1PA2_dup2436" "L1PA3_dup5468"
## [261] "L1PA3_dup9856" "L1PA3_dup10176" "L1PA2_dup3615" "L1PA3_dup2272"
## [265] "L1PA3_dup6584" "L1PA2_dup4714" "L1PA3_dup6573" "L1PA3_dup165"
## [269] "L1HS_dup787" "L1PA3_dup7893" "L1PA2_dup530" "L1PA3_dup5866"
## [273] "L1PA2_dup2408" "L1HS_dup831" "L1PA3_dup2620" "L1HS_dup270"
## [277] "L1PA3_dup1952" "L1PA2_dup3742" "L1PA2_dup4791" "L1PA3_dup4688"
## [281] "L1HS_dup244" "L1HS_dup35" "L1PA2_dup2988" "L1PA2_dup635"
## [285] "L1PA3_dup4122" "L1PA2_dup3439" "L1PA3_dup9255" "L1PA3_dup3507"
## [289] "L1PA2_dup1968" "L1PA3_dup3954" "L1PA2_dup759" "L1PA2_dup4775"
## [293] "L1PA3_dup6434" "L1PA2_dup1049" "L1HS_dup1077" "L1PA2_dup2271"
## [297] "L1HS_dup138" "L1PA3_dup1943" "L1PA3_dup9734" "L1PA3_dup3509"
## [301] "L1PA3_dup5594" "L1HS_dup1339" "L1PA3_dup7237" "L1PA2_dup3579"
## [305] "L1PA2_dup2127" "L1PA2_dup1560" "L1PA3_dup5207" "L1PA2_dup3881"
## [309] "L1PA3_dup748" "L1HS_dup429" "L1PA3_dup1279" "L1HS_dup1478"
## [313] "L1PA3_dup2389" "L1HS_dup679" "L1PA2_dup1426" "L1PA3_dup5418"
## [317] "L1PA2_dup1331" "L1PA3_dup2662" "L1PA3_dup4603" "L1PA2_dup4053"
## [321] "L1PA3_dup4259" "L1PA3_dup10011" "L1PA2_dup747" "L1HS_dup1342"
## [325] "L1PA2_dup1375" "L1PA2_dup1418" "L1PA2_dup4901" "L1PA2_dup3773"
## [329] "L1PA3_dup1770" "L1PA2_dup4652" "L1HS_dup1357" "L1PA3_dup4349"
## [333] "L1PA3_dup2683" "L1HS_dup143" "L1HS_dup1437" "L1PA3_dup345"
## [337] "L1PA2_dup4838" "L1PA2_dup1050" "L1PA3_dup6387" "L1PA3_dup9373"
## [341] "L1PA2_dup472" "L1PA3_dup10096" "L1PA2_dup326" "L1PA2_dup3622"
## [345] "L1PA3_dup1550" "L1HS_dup87" "L1PA3_dup3153" "L1PA2_dup3629"
## [349] "L1PA2_dup3425" "L1PA3_dup10043" "L1PA2_dup1978" "L1HS_dup405"
## [353] "L1PA3_dup3005" "L1PA2_dup4639" "L1PA2_dup2295" "L1PA2_dup4421"
## [357] "L1PA2_dup4262" "L1HS_dup1020" "L1PA3_dup5047" "L1PA2_dup360"
## [361] "L1HS_dup743" "L1PA2_dup1760" "L1PA3_dup10072" "L1PA3_dup8328"
## [365] "L1PA3_dup3863" "L1PA2_dup4378" "L1HS_dup466" "L1PA3_dup5540"
## [369] "L1PA3_dup638" "L1HS_dup1104" "L1HS_dup90" "L1PA2_dup358"
## [373] "L1PA2_dup4237" "L1HS_dup225" "L1PA3_dup5355" "L1PA2_dup629"
## [377] "L1PA2_dup196" "L1PA3_dup6929" "L1PA2_dup2430" "L1PA2_dup2444"
## [381] "L1PA2_dup4776" "L1HS_dup907" "L1PA3_dup8891" "L1PA2_dup3445"
## [385] "L1PA2_dup2537" "L1PA2_dup4201" "L1HS_dup204" "L1PA2_dup2496"
## [389] "L1PA3_dup6436" "L1HS_dup1243" "L1PA2_dup2047" "L1PA2_dup1177"
## [393] "L1HS_dup1491" "L1PA3_dup8310" "L1PA3_dup7637" "L1PA3_dup7432"
## [397] "L1PA2_dup4441" "L1PA3_dup9702" "L1PA2_dup2282" "L1PA3_dup9946"
## [401] "L1PA3_dup7792" "L1HS_dup163" "L1PA3_dup3404" "L1PA2_dup805"
## [405] "L1HS_dup600" "L1HS_dup1019" "L1PA2_dup4045" "L1PA2_dup732"
## [409] "L1PA2_dup4335" "L1PA3_dup1727" "L1PA3_dup6966" "L1PA3_dup9202"
## [413] "L1PA3_dup3959" "L1PA3_dup1988" "L1HS_dup596" "L1PA3_dup7947"
## [417] "L1PA2_dup3042" "L1PA3_dup4391" "L1PA2_dup3283" "L1PA2_dup1078"
## [421] "L1PA2_dup2581" "L1PA2_dup4478" "L1PA2_dup413" "L1PA3_dup1647"
## [425] "L1PA2_dup2004" "L1HS_dup811" "L1PA2_dup2729" "L1HS_dup370"
## [429] "L1PA3_dup7840" "L1PA2_dup4454" "L1PA3_dup10531" "L1PA3_dup3950"
## [433] "L1PA3_dup1027" "L1PA2_dup3003" "L1PA2_dup4226" "L1PA3_dup247"
## [437] "L1PA2_dup2876" "L1PA3_dup6871" "L1PA3_dup7316" "L1PA3_dup4596"
## [441] "L1PA2_dup3503" "L1HS_dup802" "L1PA2_dup98" "L1PA2_dup3426"
## [445] "L1PA3_dup5886" "L1HS_dup803" "L1PA3_dup8520" "L1HS_dup1284"
## [449] "L1PA3_dup5057" "L1PA3_dup3291" "L1PA3_dup2755" "L1PA3_dup8896"
## [453] "L1PA3_dup6112" "L1PA2_dup514" "L1PA2_dup3160" "L1PA2_dup1653"
## [457] "L1PA2_dup4430" "L1PA3_dup683" "L1PA3_dup6730" "L1HS_dup579"
## [461] "L1HS_dup62" "L1PA2_dup2089" "L1PA3_dup5238" "L1PA2_dup2504"
## [465] "L1PA3_dup6884" "L1PA2_dup3930" "L1PA2_dup3766" "L1PA3_dup8117"
## [469] "L1PA3_dup4408" "L1PA3_dup1463" "L1PA2_dup1463" "L1PA2_dup684"
## [473] "L1PA3_dup1046" "L1PA2_dup2254" "L1HS_dup1501" "L1PA3_dup3484"
## [477] "L1PA2_dup678" "L1PA3_dup3729" "L1PA2_dup4389" "L1PA3_dup5510"
## [481] "L1PA2_dup365" "L1PA2_dup1112" "L1PA3_dup2039" "L1PA3_dup7288"
## [485] "L1PA3_dup1114" "L1PA3_dup2643" "L1PA2_dup383" "L1PA2_dup4367"
## [489] "L1PA3_dup5927" "L1PA2_dup1023" "L1PA2_dup4043" "L1PA3_dup6523"
## [493] "L1PA2_dup2577" "L1PA2_dup4612" "L1PA2_dup1058" "L1PA3_dup3880"
## [497] "L1PA3_dup1026" "L1PA3_dup7605" "L1PA2_dup2261" "L1HS_dup1514"
## [501] "L1PA2_dup798" "L1PA3_dup5363" "L1HS_dup1616" "L1PA3_dup840"
## [505] "L1PA3_dup8313" "L1PA3_dup1328" "L1PA2_dup4611" "L1HS_dup622"
## [509] "L1HS_dup1295" "L1PA2_dup307" "L1PA2_dup1992" "L1PA2_dup1248"
## [513] "L1PA3_dup1337" "L1PA2_dup4432" "L1PA2_dup4713" "L1PA3_dup4393"
## [517] "L1PA3_dup5825" "L1PA3_dup6160" "L1PA3_dup9722" "L1PA3_dup9866"
asap_heatmap_snRNA(region = c("PFC"),
tes = data_TE_annotation[which(data_TE_annotation$type == "HERV"),"TE_id"],
return_df = F,
breaks = seq(0,15,length.out = 52),
data = TE_data,
group_cols = c("celltype"),
index_row_reorder = c(HERVs_sorted_pfc),
order_cols_groups = order_cols_celltype,
title = "PFC HERV: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
annotation_cols = annotation_cols)

## $heatmap
##
## $order_cols
## [1] "AA_ASAP116_PD_NP22-55_PFC_0" "ASAP155_ctrl_NP23-21_PFC_0"
## [3] "AA_ASAP151_PD_NP17-232_PFC_0" "AA_ASAP90_ctrl_NP16-293_PFC_0"
## [5] "AA_ASAP89_ctrl_NP16-284_PFC_0" "AA_ASAP153_ctrl_NP19-137_PFC_0"
## [7] "AA_ASAP83_NP16-119_ctrl_PFC_0" "AA_ASAP152_PD_NP19-91_PFC_0"
## [9] "MJ_ASAP14_ctrl_NP16-164_PFC_0" "DA480_ASAP15_ctrl_NP16-21_PFC_0"
## [11] "AA_ASAP86_NP18-148_ctrl_PFC_0" "AA_ASAP80_PD_NP21-57_PFC_0"
## [13] "DA777_ASAP28_PD_NP17-191_PFC_0" "DA809_ASAP30_PD_NP18-117_PFC_0"
## [15] "DA430_ASAP9_PD_NP16-162_PFC_0" "AA_ASAP82_PD_NP21-217_PFC_0"
## [17] "DA509_ASAP36_PD_NP19-16_PFC_0" "DA490_ASAP11_PD_P73_PFC_0"
## [19] "DA810_ASAP34_PD_NP18-304_PFC_0" "DA428_ASAP13_ctrl_NP16-161_PFC_0"
## [21] "DA488_ASAP16_ctrl_PT231_PFC_0" "DA499_ASAP44_PD_NP19-255_PFC_0"
## [23] "DA432_ASAP12_PD_P74_PFC_0" "DA806_ASAP58_ctrl_NP19-45_PFC_0"
## [25] "DA476_ASAP10_PD_NP16-25_PFC_0" "DA795_ASAP55_ctrl_NP19-37_PFC_0"
## [27] "AA_ASAP145_ctrl_NP19-218_PFC_0" "AA_ASAP85_NP18-46_ctrl_PFC_0"
## [29] "AA_ASAP91_ctrl_NP17-20_PFC_0" "AA_ASAP81_PD_NP21-208_PFC_0"
## [31] "DA775_ASAP22_PD_NP16-269_PFC_0" "DA804_ASAP49_ctrl_NP18-159_PFC_0"
## [33] "DA813_ASAP17_PD_NP16-140_PFC_0" "DA480_ASAP15_ctrl_NP16-21_PFC_1"
## [35] "AA_ASAP85_NP18-46_ctrl_PFC_1" "DA795_ASAP55_ctrl_NP19-37_PFC_1"
## [37] "AA_ASAP153_ctrl_NP19-137_PFC_1" "AA_ASAP91_ctrl_NP17-20_PFC_1"
## [39] "ASAP155_ctrl_NP23-21_PFC_1" "AA_ASAP90_ctrl_NP16-293_PFC_1"
## [41] "AA_ASAP89_ctrl_NP16-284_PFC_1" "MJ_ASAP14_ctrl_NP16-164_PFC_1"
## [43] "AA_ASAP116_PD_NP22-55_PFC_1" "AA_ASAP151_PD_NP17-232_PFC_1"
## [45] "AA_ASAP145_ctrl_NP19-218_PFC_1" "DA476_ASAP10_PD_NP16-25_PFC_1"
## [47] "DA777_ASAP28_PD_NP17-191_PFC_1" "DA430_ASAP9_PD_NP16-162_PFC_1"
## [49] "AA_ASAP83_NP16-119_ctrl_PFC_1" "DA809_ASAP30_PD_NP18-117_PFC_1"
## [51] "DA490_ASAP11_PD_P73_PFC_1" "AA_ASAP82_PD_NP21-217_PFC_1"
## [53] "DA509_ASAP36_PD_NP19-16_PFC_1" "AA_ASAP81_PD_NP21-208_PFC_1"
## [55] "AA_ASAP86_NP18-148_ctrl_PFC_1" "AA_ASAP80_PD_NP21-57_PFC_1"
## [57] "DA499_ASAP44_PD_NP19-255_PFC_1" "DA432_ASAP12_PD_P74_PFC_1"
## [59] "AA_ASAP152_PD_NP19-91_PFC_1" "DA428_ASAP13_ctrl_NP16-161_PFC_1"
## [61] "DA806_ASAP58_ctrl_NP19-45_PFC_1" "DA810_ASAP34_PD_NP18-304_PFC_1"
## [63] "DA488_ASAP16_ctrl_PT231_PFC_1" "DA775_ASAP22_PD_NP16-269_PFC_1"
## [65] "DA804_ASAP49_ctrl_NP18-159_PFC_1" "AA_ASAP82_PD_NP21-217_PFC_2"
## [67] "AA_ASAP90_ctrl_NP16-293_PFC_2" "AA_ASAP152_PD_NP19-91_PFC_2"
## [69] "DA428_ASAP13_ctrl_NP16-161_PFC_2" "DA499_ASAP44_PD_NP19-255_PFC_2"
## [71] "DA810_ASAP34_PD_NP18-304_PFC_2" "DA806_ASAP58_ctrl_NP19-45_PFC_2"
## [73] "DA488_ASAP16_ctrl_PT231_PFC_2" "AA_ASAP86_NP18-148_ctrl_PFC_2"
## [75] "DA480_ASAP15_ctrl_NP16-21_PFC_2" "AA_ASAP145_ctrl_NP19-218_PFC_2"
## [77] "DA476_ASAP10_PD_NP16-25_PFC_2" "MJ_ASAP14_ctrl_NP16-164_PFC_2"
## [79] "DA430_ASAP9_PD_NP16-162_PFC_2" "ASAP155_ctrl_NP23-21_PFC_2"
## [81] "AA_ASAP116_PD_NP22-55_PFC_2" "AA_ASAP80_PD_NP21-57_PFC_2"
## [83] "AA_ASAP83_NP16-119_ctrl_PFC_2" "AA_ASAP89_ctrl_NP16-284_PFC_2"
## [85] "DA795_ASAP55_ctrl_NP19-37_PFC_2" "DA432_ASAP12_PD_P74_PFC_2"
## [87] "DA509_ASAP36_PD_NP19-16_PFC_2" "DA490_ASAP11_PD_P73_PFC_2"
## [89] "AA_ASAP81_PD_NP21-208_PFC_2" "AA_ASAP154_ctrl_NP21-04_PFC_2"
## [91] "AA_ASAP153_ctrl_NP19-137_PFC_2" "AA_ASAP91_ctrl_NP17-20_PFC_2"
## [93] "AA_ASAP84_NP17-216_ctrl_PFC_2" "DA785_ASAP47_ctrl_NP17-256_PFC_2"
## [95] "AA_ASAP150_PD_NP16-285_PFC_2" "DA809_ASAP30_PD_NP18-117_PFC_2"
## [97] "AA_ASAP151_PD_NP17-232_PFC_2" "DA804_ASAP49_ctrl_NP18-159_PFC_2"
## [99] "DA775_ASAP22_PD_NP16-269_PFC_2" "DA808_ASAP41_PD_NP19-108_PFC_2"
## [101] "DA490_ASAP11_PD_P73_PFC_3" "DA509_ASAP36_PD_NP19-16_PFC_3"
## [103] "AA_ASAP90_ctrl_NP16-293_PFC_3" "AA_ASAP154_ctrl_NP21-04_PFC_3"
## [105] "AA_ASAP86_NP18-148_ctrl_PFC_3" "AA_ASAP152_PD_NP19-91_PFC_3"
## [107] "ASAP155_ctrl_NP23-21_PFC_3" "DA480_ASAP15_ctrl_NP16-21_PFC_3"
## [109] "AA_ASAP116_PD_NP22-55_PFC_3" "DA785_ASAP47_ctrl_NP17-256_PFC_3"
## [111] "MJ_ASAP14_ctrl_NP16-164_PFC_3" "AA_ASAP151_PD_NP17-232_PFC_3"
## [113] "AA_ASAP89_ctrl_NP16-284_PFC_3" "AA_ASAP83_NP16-119_ctrl_PFC_3"
## [115] "AA_ASAP82_PD_NP21-217_PFC_3" "DA499_ASAP44_PD_NP19-255_PFC_3"
## [117] "AA_ASAP80_PD_NP21-57_PFC_3" "DA777_ASAP28_PD_NP17-191_PFC_3"
## [119] "DA806_ASAP58_ctrl_NP19-45_PFC_3" "DA810_ASAP34_PD_NP18-304_PFC_3"
## [121] "DA488_ASAP16_ctrl_PT231_PFC_3" "DA428_ASAP13_ctrl_NP16-161_PFC_3"
## [123] "DA430_ASAP9_PD_NP16-162_PFC_3" "DA809_ASAP30_PD_NP18-117_PFC_3"
## [125] "DA804_ASAP49_ctrl_NP18-159_PFC_3" "DA476_ASAP10_PD_NP16-25_PFC_3"
## [127] "DA795_ASAP55_ctrl_NP19-37_PFC_3" "DA775_ASAP22_PD_NP16-269_PFC_3"
## [129] "AA_ASAP91_ctrl_NP17-20_PFC_3" "AA_ASAP84_NP17-216_ctrl_PFC_3"
## [131] "DA432_ASAP12_PD_P74_PFC_3" "AA_ASAP150_PD_NP16-285_PFC_3"
## [133] "AA_ASAP145_ctrl_NP19-218_PFC_3" "AA_ASAP147_ctrl_NP22-37_PFC_5"
## [135] "DA480_ASAP15_ctrl_NP16-21_PFC_5" "AA_ASAP89_ctrl_NP16-284_PFC_5"
## [137] "AA_ASAP90_ctrl_NP16-293_PFC_5" "AA_ASAP85_NP18-46_ctrl_PFC_5"
## [139] "DA490_ASAP11_PD_P73_PFC_5" "DA509_ASAP36_PD_NP19-16_PFC_5"
## [141] "DA430_ASAP9_PD_NP16-162_PFC_5" "AA_ASAP91_ctrl_NP17-20_PFC_5"
## [143] "AA_ASAP83_NP16-119_ctrl_PFC_5" "DA775_ASAP22_PD_NP16-269_PFC_5"
## [145] "DA806_ASAP58_ctrl_NP19-45_PFC_5" "DA428_ASAP13_ctrl_NP16-161_PFC_5"
## [147] "DA777_ASAP28_PD_NP17-191_PFC_5" "DA499_ASAP44_PD_NP19-255_PFC_5"
## [149] "DA810_ASAP34_PD_NP18-304_PFC_5" "DA488_ASAP16_ctrl_PT231_PFC_5"
## [151] "AA_ASAP82_PD_NP21-217_PFC_5" "AA_ASAP80_PD_NP21-57_PFC_5"
## [153] "AA_ASAP86_NP18-148_ctrl_PFC_5" "AA_ASAP152_PD_NP19-91_PFC_5"
## [155] "ASAP155_ctrl_NP23-21_PFC_5" "MJ_ASAP14_ctrl_NP16-164_PFC_5"
## [157] "DA785_ASAP47_ctrl_NP17-256_PFC_5" "AA_ASAP84_NP17-216_ctrl_PFC_5"
## [159] "AA_ASAP154_ctrl_NP21-04_PFC_5" "DA799_ASAP19_PD_NP16-160_PFC_5"
## [161] "DA432_ASAP12_PD_P74_PFC_5" "AA_ASAP153_ctrl_NP19-137_PFC_5"
## [163] "DA813_ASAP17_PD_NP16-140_PFC_5" "AA_ASAP116_PD_NP22-55_PFC_5"
## [165] "DA808_ASAP41_PD_NP19-108_PFC_5" "AA_ASAP150_PD_NP16-285_PFC_5"
## [167] "AA_ASAP151_PD_NP17-232_PFC_5" "DA804_ASAP49_ctrl_NP18-159_PFC_5"
## [169] "DA476_ASAP10_PD_NP16-25_PFC_5" "DA795_ASAP55_ctrl_NP19-37_PFC_5"
## [171] "AA_ASAP145_ctrl_NP19-218_PFC_5" "DA809_ASAP30_PD_NP18-117_PFC_5"
## [173] "DA430_ASAP9_PD_NP16-162_PFC_4" "AA_ASAP89_ctrl_NP16-284_PFC_4"
## [175] "DA428_ASAP13_ctrl_NP16-161_PFC_4" "AA_ASAP152_PD_NP19-91_PFC_4"
## [177] "AA_ASAP151_PD_NP17-232_PFC_4" "DA806_ASAP58_ctrl_NP19-45_PFC_4"
## [179] "AA_ASAP83_NP16-119_ctrl_PFC_4" "DA488_ASAP16_ctrl_PT231_PFC_4"
## [181] "AA_ASAP80_PD_NP21-57_PFC_4" "DA480_ASAP15_ctrl_NP16-21_PFC_4"
## [183] "ASAP155_ctrl_NP23-21_PFC_4" "AA_ASAP145_ctrl_NP19-218_PFC_4"
## [185] "MJ_ASAP14_ctrl_NP16-164_PFC_4" "AA_ASAP90_ctrl_NP16-293_PFC_4"
## [187] "DA499_ASAP44_PD_NP19-255_PFC_4" "AA_ASAP82_PD_NP21-217_PFC_4"
## [189] "DA775_ASAP22_PD_NP16-269_PFC_4" "AA_ASAP86_NP18-148_ctrl_PFC_4"
## [191] "DA432_ASAP12_PD_P74_PFC_4" "DA490_ASAP11_PD_P73_PFC_4"
## [193] "DA808_ASAP41_PD_NP19-108_PFC_4" "DA804_ASAP49_ctrl_NP18-159_PFC_4"
## [195] "DA795_ASAP55_ctrl_NP19-37_PFC_4" "AA_ASAP116_PD_NP22-55_PFC_4"
## [197] "DA476_ASAP10_PD_NP16-25_PFC_4" "DA785_ASAP47_ctrl_NP17-256_PFC_6"
## [199] "MJ_ASAP14_ctrl_NP16-164_PFC_6" "AA_ASAP152_PD_NP19-91_PFC_6"
## [201] "AA_ASAP89_ctrl_NP16-284_PFC_6" "DA428_ASAP13_ctrl_NP16-161_PFC_6"
##
## $order_rows
## [1] "HERV_dup773" "HERV_dup1758" "HERV_dup631" "HERV_dup288" "HERV_dup3252"
## [6] "HERV_dup152" "HERV_dup2491" "HERV_dup3390" "HERV_dup1281" "HERV_dup2856"
## [11] "HERV_dup1708" "HERV_dup600" "HERV_dup1209" "HERV_dup1" "HERV_dup1079"
## [16] "HERV_dup302" "HERV_dup2841" "HERV_dup2966" "HERV_dup2838" "HERV_dup265"
## [21] "HERV_dup1050" "HERV_dup2880" "HERV_dup3357" "HERV_dup1702" "HERV_dup2273"
## [26] "HERV_dup1000" "HERV_dup614" "HERV_dup470" "HERV_dup1283" "HERV_dup940"
## [31] "HERV_dup799" "HERV_dup3226" "HERV_dup54" "HERV_dup1888" "HERV_dup2900"
## [36] "HERV_dup384" "HERV_dup1339" "HERV_dup1669" "HERV_dup2381" "HERV_dup1357"
## [41] "HERV_dup1102" "HERV_dup209" "HERV_dup2789" "HERV_dup926" "HERV_dup3171"
## [46] "HERV_dup379" "HERV_dup1456" "HERV_dup3174" "HERV_dup417" "HERV_dup2365"
## [51] "HERV_dup2182" "HERV_dup1004" "HERV_dup112" "HERV_dup916" "HERV_dup717"
## [56] "HERV_dup1356" "HERV_dup3105" "HERV_dup980" "HERV_dup1308" "HERV_dup3423"
## [61] "HERV_dup1243" "HERV_dup3379" "HERV_dup93" "HERV_dup37" "HERV_dup2012"
## [66] "HERV_dup1701" "HERV_dup3355" "HERV_dup3248" "HERV_dup3363" "HERV_dup3673"
## [71] "HERV_dup3266" "HERV_dup1319" "HERV_dup474" "HERV_dup1203" "HERV_dup2106"
## [76] "HERV_dup1208" "HERV_dup2376" "HERV_dup1309" "HERV_dup1272" "HERV_dup1657"
## [81] "HERV_dup1362" "HERV_dup1002" "HERV_dup3375" "HERV_dup873" "HERV_dup1310"
## [86] "HERV_dup612" "HERV_dup110" "HERV_dup2529" "HERV_dup904" "HERV_dup670"
## [91] "HERV_dup1598" "HERV_dup562" "HERV_dup1255" "HERV_dup1327" "HERV_dup880"
## [96] "HERV_dup1663" "HERV_dup565" "HERV_dup1038" "HERV_dup2292" "HERV_dup1724"
## [101] "HERV_dup518" "HERV_dup2879" "HERV_dup682" "HERV_dup1371" "HERV_dup831"
## [106] "HERV_dup3343" "HERV_dup913" "HERV_dup731" "HERV_dup1382" "HERV_dup1670"
## [111] "HERV_dup1447" "HERV_dup151" "HERV_dup1934" "HERV_dup2840" "HERV_dup1359"
## [116] "HERV_dup1048" "HERV_dup1307" "HERV_dup1449" "HERV_dup1749" "HERV_dup597"
## [121] "HERV_dup2176" "HERV_dup2261" "HERV_dup1944" "HERV_dup739" "HERV_dup2599"
## [126] "HERV_dup2217" "HERV_dup1334" "HERV_dup1315" "HERV_dup899" "HERV_dup348"
## [131] "HERV_dup57" "HERV_dup293" "HERV_dup1755" "HERV_dup1282" "HERV_dup355"
## [136] "HERV_dup2894" "HERV_dup1001" "HERV_dup2902" "HERV_dup2550" "HERV_dup2137"
## [141] "HERV_dup1667" "HERV_dup1875" "HERV_dup969" "HERV_dup1351" "HERV_dup2914"
## [146] "HERV_dup1694" "HERV_dup3107" "HERV_dup758" "HERV_dup966" "HERV_dup2299"
## [151] "HERV_dup1776" "HERV_dup26" "HERV_dup2631" "HERV_dup3522" "HERV_dup1935"
## [156] "HERV_dup1345" "HERV_dup1611" "HERV_dup1052" "HERV_dup292" "HERV_dup1512"
## [161] "HERV_dup2843" "HERV_dup613" "HERV_dup2877" "HERV_dup1107" "HERV_dup3212"
## [166] "HERV_dup1269" "HERV_dup1081" "HERV_dup1932" "HERV_dup2530" "HERV_dup1364"
## [171] "HERV_dup1017" "HERV_dup2166" "HERV_dup301" "HERV_dup5" "HERV_dup3418"
## [176] "HERV_dup369" "HERV_dup954" "HERV_dup1007" "HERV_dup1940" "HERV_dup380"
## [181] "HERV_dup1750" "HERV_dup2643" "HERV_dup1303" "HERV_dup1253" "HERV_dup65"
## [186] "HERV_dup1232" "HERV_dup3196" "HERV_dup967" "HERV_dup2566" "HERV_dup508"
## [191] "HERV_dup2834" "HERV_dup876" "HERV_dup1756" "HERV_dup1569" "HERV_dup1358"
## [196] "HERV_dup3270" "HERV_dup203" "HERV_dup1302" "HERV_dup2589" "HERV_dup1416"
## [201] "HERV_dup872" "HERV_dup2438" "HERV_dup3217" "HERV_dup2719" "HERV_dup487"
## [206] "HERV_dup3033" "HERV_dup3417" "HERV_dup1613" "HERV_dup939" "HERV_dup3140"
## [211] "HERV_dup2163" "HERV_dup482" "HERV_dup2662" "HERV_dup1242" "HERV_dup2266"
## [216] "HERV_dup777" "HERV_dup291" "HERV_dup3580" "HERV_dup3050" "HERV_dup2250"
## [221] "HERV_dup3198" "HERV_dup1295" "HERV_dup2235" "HERV_dup2412" "HERV_dup471"
## [226] "HERV_dup2939" "HERV_dup443" "HERV_dup202" "HERV_dup2188" "HERV_dup1484"
## [231] "HERV_dup1046" "HERV_dup290" "HERV_dup1890" "HERV_dup215" "HERV_dup3694"
## [236] "HERV_dup3529" "HERV_dup1617" "HERV_dup36" "HERV_dup2736" "HERV_dup3231"
## [241] "HERV_dup2936" "HERV_dup1049" "HERV_dup1520" "HERV_dup34" "HERV_dup399"
## [246] "HERV_dup3251" "HERV_dup468" "HERV_dup979" "HERV_dup990" "HERV_dup2803"
## [251] "HERV_dup2500" "HERV_dup2319" "HERV_dup3187" "HERV_dup433" "HERV_dup1036"
## [256] "HERV_dup1605" "HERV_dup1707" "HERV_dup2752" "HERV_dup2857" "HERV_dup2963"
## [261] "HERV_dup2623" "HERV_dup282" "HERV_dup2961" "HERV_dup2964" "HERV_dup3505"
## [266] "HERV_dup1662" "HERV_dup441" "HERV_dup2735" "HERV_dup329" "HERV_dup2905"
## [271] "HERV_dup890" "HERV_dup949" "HERV_dup1661" "HERV_dup2915" "HERV_dup586"
## [276] "HERV_dup3124" "HERV_dup27" "HERV_dup2978" "HERV_dup1917" "HERV_dup1596"
## [281] "HERV_dup249" "HERV_dup2111" "HERV_dup870" "HERV_dup1717" "HERV_dup94"
## [286] "HERV_dup2093" "HERV_dup2588" "HERV_dup251" "HERV_dup2464" "HERV_dup1112"
## [291] "HERV_dup1073" "HERV_dup18" "HERV_dup3286" "HERV_dup1240" "HERV_dup3341"
## [296] "HERV_dup1658" "HERV_dup2179" "HERV_dup1331" "HERV_dup118" "HERV_dup3358"
## [301] "HERV_dup505" "HERV_dup3143" "HERV_dup2769" "HERV_dup2801" "HERV_dup2784"
## [306] "HERV_dup2264" "HERV_dup1846" "HERV_dup2603" "HERV_dup1437" "HERV_dup2353"
## [311] "HERV_dup1780" "HERV_dup377" "HERV_dup1298" "HERV_dup1324" "HERV_dup1972"
## [316] "HERV_dup2847" "HERV_dup968" "HERV_dup2129" "HERV_dup956" "HERV_dup3118"
## [321] "HERV_dup2646" "HERV_dup2476" "HERV_dup1317" "HERV_dup1851" "HERV_dup492"
## [326] "HERV_dup1316" "HERV_dup1703" "HERV_dup1236" "HERV_dup2812" "HERV_dup2878"
## [331] "HERV_dup2733" "HERV_dup2415" "HERV_dup2533" "HERV_dup58" "HERV_dup2480"
## [336] "HERV_dup1321" "HERV_dup250" "HERV_dup2855" "HERV_dup3406" "HERV_dup2130"
## [341] "HERV_dup1374" "HERV_dup724" "HERV_dup2149" "HERV_dup23" "HERV_dup2562"
## [346] "HERV_dup2607" "HERV_dup1089" "HERV_dup1187" "HERV_dup2298" "HERV_dup3020"
## [351] "HERV_dup2695" "HERV_dup1982" "HERV_dup469" "HERV_dup1071" "HERV_dup1579"
## [356] "HERV_dup1401" "HERV_dup1268" "HERV_dup2337" "HERV_dup1673" "HERV_dup599"
## [361] "HERV_dup1719" "HERV_dup3148" "HERV_dup2886" "HERV_dup1491" "HERV_dup1847"
## [366] "HERV_dup2747" "HERV_dup2941" "HERV_dup573" "HERV_dup3459" "HERV_dup344"
## [371] "HERV_dup661" "HERV_dup2303" "HERV_dup3410" "HERV_dup1064" "HERV_dup1923"
## [376] "HERV_dup1720" "HERV_dup29" "HERV_dup409" "HERV_dup1322" "HERV_dup331"
## [381] "HERV_dup1931" "HERV_dup1920" "HERV_dup2085" "HERV_dup1943" "HERV_dup2192"
## [386] "HERV_dup1210" "HERV_dup388" "HERV_dup2282" "HERV_dup1731" "HERV_dup1389"
## [391] "HERV_dup1500" "HERV_dup1671" "HERV_dup2183" "HERV_dup2187" "HERV_dup1438"
## [396] "HERV_dup1005" "HERV_dup2598" "HERV_dup3342" "HERV_dup180" "HERV_dup2730"
## [401] "HERV_dup1394" "HERV_dup3063" "HERV_dup1804" "HERV_dup1730" "HERV_dup2561"
## [406] "HERV_dup729" "HERV_dup300" "HERV_dup1350" "HERV_dup2907" "HERV_dup3365"
## [411] "HERV_dup467" "HERV_dup850" "HERV_dup386" "HERV_dup2436" "HERV_dup214"
## [416] "HERV_dup1201" "HERV_dup2809" "HERV_dup2383" "HERV_dup1973" "HERV_dup218"
## [421] "HERV_dup1213" "HERV_dup2555" "HERV_dup3044" "HERV_dup2134" "HERV_dup2158"
## [426] "HERV_dup1629" "HERV_dup2949" "HERV_dup2518" "HERV_dup1556" "HERV_dup1218"
## [431] "HERV_dup1082" "HERV_dup665" "HERV_dup3408" "HERV_dup1541" "HERV_dup3287"
## [436] "HERV_dup2848" "HERV_dup554" "HERV_dup1823" "HERV_dup1802" "HERV_dup1638"
## [441] "HERV_dup1222" "HERV_dup1587" "HERV_dup1285" "HERV_dup2778" "HERV_dup3227"
## [446] "HERV_dup3117" "HERV_dup1378" "HERV_dup723" "HERV_dup553" "HERV_dup1297"
## [451] "HERV_dup3210" "HERV_dup1872" "HERV_dup2391" "HERV_dup2378" "HERV_dup1653"
## [456] "HERV_dup2891" "HERV_dup2112" "HERV_dup1090" "HERV_dup2962" "HERV_dup3430"
## [461] "HERV_dup3351" "HERV_dup1093" "HERV_dup1953" "HERV_dup2979" "HERV_dup632"
## [466] "HERV_dup1914" "HERV_dup2967" "HERV_dup1668" "HERV_dup1513" "HERV_dup728"
## [471] "HERV_dup1304" "HERV_dup243" "HERV_dup1333" "HERV_dup2635" "HERV_dup272"
## [476] "HERV_dup803" "HERV_dup2366" "HERV_dup336" "HERV_dup1757" "HERV_dup2379"
## [481] "HERV_dup1080" "HERV_dup1146" "HERV_dup3031" "HERV_dup2002" "HERV_dup626"
## [486] "HERV_dup1273" "HERV_dup1453" "HERV_dup933" "HERV_dup2604" "HERV_dup3507"
## [491] "HERV_dup2653" "HERV_dup662" "HERV_dup115" "HERV_dup2422" "HERV_dup2977"
## [496] "HERV_dup1889" "HERV_dup120" "HERV_dup2242" "HERV_dup3388" "HERV_dup1156"
## [501] "HERV_dup852" "HERV_dup2041" "HERV_dup1390" "HERV_dup1869" "HERV_dup1366"
## [506] "HERV_dup736" "HERV_dup2706" "HERV_dup982" "HERV_dup1933" "HERV_dup2278"
## [511] "HERV_dup2696" "HERV_dup314" "HERV_dup2027" "HERV_dup935" "HERV_dup556"
## [516] "HERV_dup909" "HERV_dup2524" "HERV_dup434" "HERV_dup1412" "HERV_dup3008"
## [521] "HERV_dup3284" "HERV_dup356" "HERV_dup3220" "HERV_dup882" "HERV_dup509"
## [526] "HERV_dup276" "HERV_dup1948" "HERV_dup1103" "HERV_dup894" "HERV_dup1891"
## [531] "HERV_dup3335" "HERV_dup1433" "HERV_dup108" "HERV_dup2290" "HERV_dup2141"
## [536] "HERV_dup577" "HERV_dup2934" "HERV_dup1245" "HERV_dup3108" "HERV_dup3179"
## [541] "HERV_dup1614" "HERV_dup2728" "HERV_dup1248" "HERV_dup2743" "HERV_dup3189"
## [546] "HERV_dup3215" "HERV_dup2548" "HERV_dup419" "HERV_dup38" "HERV_dup1108"
## [551] "HERV_dup1047" "HERV_dup703" "HERV_dup1526" "HERV_dup1381" "HERV_dup1184"
## [556] "HERV_dup2823" "HERV_dup884" "HERV_dup446" "HERV_dup3100" "HERV_dup277"
## [561] "HERV_dup2019" "HERV_dup1099" "HERV_dup746" "HERV_dup3394" "HERV_dup1129"
## [566] "HERV_dup17" "HERV_dup1029" "HERV_dup517" "HERV_dup447" "HERV_dup3319"
## [571] "HERV_dup1527" "HERV_dup2334" "HERV_dup2404" "HERV_dup851" "HERV_dup977"
## [576] "HERV_dup1114" "HERV_dup3182" "HERV_dup452" "HERV_dup2536" "HERV_dup1639"
## [581] "HERV_dup1254" "HERV_dup1403" "HERV_dup3366" "HERV_dup450" "HERV_dup321"
## [586] "HERV_dup2985" "HERV_dup710" "HERV_dup3181" "HERV_dup3416" "HERV_dup177"
## [591] "HERV_dup3137" "HERV_dup1413" "HERV_dup551" "HERV_dup1212" "HERV_dup2663"
## [596] "HERV_dup1926" "HERV_dup2272" "HERV_dup3688" "HERV_dup3328" "HERV_dup2804"
## [601] "HERV_dup776" "HERV_dup2159" "HERV_dup846" "HERV_dup3239" "HERV_dup2479"
## [606] "HERV_dup928" "HERV_dup2896" "HERV_dup2945" "HERV_dup1549" "HERV_dup1962"
## [611] "HERV_dup2772" "HERV_dup732" "HERV_dup1656" "HERV_dup2785" "HERV_dup519"
## [616] "HERV_dup772" "HERV_dup1383" "HERV_dup568" "HERV_dup570" "HERV_dup127"
## [621] "HERV_dup3481" "HERV_dup3073" "HERV_dup2033" "HERV_dup488" "HERV_dup185"
## [626] "HERV_dup184" "HERV_dup1979" "HERV_dup1417" "HERV_dup2797" "HERV_dup2152"
## [631] "HERV_dup1131" "HERV_dup39" "HERV_dup1459" "HERV_dup1172" "HERV_dup2632"
## [636] "HERV_dup1470" "HERV_dup3606" "HERV_dup1278" "HERV_dup692" "HERV_dup927"
## [641] "HERV_dup1235" "HERV_dup1557" "HERV_dup2356" "HERV_dup900" "HERV_dup578"
## [646] "HERV_dup2942" "HERV_dup2937" "HERV_dup2441" "HERV_dup1640" "HERV_dup407"
## [651] "HERV_dup61" "HERV_dup400" "HERV_dup640" "HERV_dup671" "HERV_dup3519"
## [656] "HERV_dup1182" "HERV_dup3131" "HERV_dup2739" "HERV_dup1239" "HERV_dup975"
## [661] "HERV_dup2482" "HERV_dup1494" "HERV_dup2651" "HERV_dup1013" "HERV_dup461"
## [666] "HERV_dup86" "HERV_dup1937" "HERV_dup595" "HERV_dup934" "HERV_dup530"
## [671] "HERV_dup2557" "HERV_dup2320" "HERV_dup194" "HERV_dup1496" "HERV_dup133"
## [676] "HERV_dup357" "HERV_dup3219" "HERV_dup2647" "HERV_dup1195" "HERV_dup2128"
## [681] "HERV_dup1733" "HERV_dup981" "HERV_dup350" "HERV_dup129" "HERV_dup572"
## [686] "HERV_dup389" "HERV_dup2034" "HERV_dup1655" "HERV_dup2100" "HERV_dup21"
## [691] "HERV_dup3588" "HERV_dup173" "HERV_dup1868" "HERV_dup1958" "HERV_dup1003"
## [696] "HERV_dup634" "HERV_dup930" "HERV_dup1014" "HERV_dup1346" "HERV_dup1514"
## [701] "HERV_dup201" "HERV_dup1532" "HERV_dup591" "HERV_dup2481" "HERV_dup1664"
## [706] "HERV_dup183" "HERV_dup2620" "HERV_dup1440" "HERV_dup3013" "HERV_dup2680"
## [711] "HERV_dup2655" "HERV_dup3607" "HERV_dup1555" "HERV_dup1279" "HERV_dup1384"
## [716] "HERV_dup3015" "HERV_dup2897" "HERV_dup1228" "HERV_dup2525" "HERV_dup2972"
## [721] "HERV_dup1415" "HERV_dup1711" "HERV_dup1778" "HERV_dup1902" "HERV_dup398"
## [726] "HERV_dup735" "HERV_dup3154" "HERV_dup3545" "HERV_dup2324" "HERV_dup84"
## [731] "HERV_dup2602" "HERV_dup381" "HERV_dup1752" "HERV_dup2875" "HERV_dup3037"
## [736] "HERV_dup240" "HERV_dup3016" "HERV_dup78" "HERV_dup924"
asap_heatmap_snRNA(region = c("PUT"),
tes = data_TE_annotation[which(data_TE_annotation$type == "HERV"),"TE_id"],
return_df = F,
breaks = seq(0,15,length.out = 52),
data = TE_data,
group_cols = c("celltype"),
index_row_reorder = c(HERVs_sorted_put),
order_cols_groups = order_cols_celltype,
title = "PUT HERV: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
annotation_cols = annotation_cols)

## $heatmap
##
## $order_cols
## [1] "AA82_ASAP68_PD_NP18-117_PUT_0" "AA71_ASAP70_PD_NP18-304_PUT_0"
## [3] "AA87_ASAP76_ctrl_NP18-159_PUT_0" "AA74_ASAP62_PD_NP16-140_PUT_0"
## [5] "AA_ASAP138_PD_NP16-285_PUT_0" "AA_ASAP98_ctrl_NP16-119_PUT_0"
## [7] "AA_ASAP141_ctrl_NP19-218_PUT_0" "AA_ASAP97_PD_NP21-57_PUT_0"
## [9] "AA79_ASAP64_PD_NP16-162_PUT_0" "AA_ASAP100_ctrl_NP18-148_PUT_0"
## [11] "AA84_ASAP71_PD_NP19-16_PUT_0" "AA_ASAP92_ctrl_NP16-284_PUT_1"
## [13] "AA_ASAP139_PD_NP17-232_PUT_1" "AA79_ASAP64_PD_NP16-162_PUT_1"
## [15] "AA_ASAP144_PD_NP19-137_PUT_1" "AA_ASAP100_ctrl_NP18-148_PUT_1"
## [17] "AA74_ASAP62_PD_NP16-140_PUT_1" "AA87_ASAP76_ctrl_NP18-159_PUT_1"
## [19] "AA_ASAP88_PD_NP21-217_PUT_1" "AA71_ASAP70_PD_NP18-304_PUT_1"
## [21] "AA84_ASAP71_PD_NP19-16_PUT_1" "AA_ASAP117_PD_NP22-55_PUT_1"
## [23] "AA_ASAP87_PD_NP21-208_PUT_1" "AA83_ASAP69_PD_NP18-287_PUT_2"
## [25] "AA77_ASAP61_PD_NP16-25_PUT_2" "AA_ASAP93_ctrl_NP16-293_PUT_2"
## [27] "AA86_ASAP73_PD_NP19-108_PUT_2" "AA73_ASAP65_PD_NP16-269_PUT_2"
## [29] "AA81_ASAP67_PD_NP17-191_PUT_2" "AA_ASAP96_ctrl_NP18-46_PUT_2"
## [31] "AA_ASAP141_ctrl_NP19-218_PUT_2" "AA_ASAP140_PD_NP19-91_PUT_2"
## [33] "AA85_ASAP72_PD_NP19-23_PUT_2" "AA_ASAP88_PD_NP21-217_PUT_2"
## [35] "AA82_ASAP68_PD_NP18-117_PUT_2" "AA76_ASAP74_PD_NP19-255_PUT_2"
## [37] "AA71_ASAP70_PD_NP18-304_PUT_2" "AA_ASAP87_PD_NP21-208_PUT_2"
## [39] "AA87_ASAP76_ctrl_NP18-159_PUT_2" "AA_ASAP100_ctrl_NP18-148_PUT_2"
## [41] "AA74_ASAP62_PD_NP16-140_PUT_2" "AA84_ASAP71_PD_NP19-16_PUT_2"
## [43] "AA_ASAP97_PD_NP21-57_PUT_2" "AA_ASAP138_PD_NP16-285_PUT_2"
## [45] "AA_ASAP144_PD_NP19-137_PUT_2" "AA79_ASAP64_PD_NP16-162_PUT_2"
## [47] "AA_ASAP117_PD_NP22-55_PUT_2" "AA_ASAP98_ctrl_NP16-119_PUT_2"
## [49] "AA_ASAP139_PD_NP17-232_PUT_2" "AA_ASAP92_ctrl_NP16-284_PUT_2"
## [51] "AA88_ASAP77_ctrl_NP19-36_PUT_2" "AA_ASAP94_ctrl_NP17-20_PUT_2"
## [53] "AA89_ASAP78_ctrl_NP19-37_PUT_2" "AA_ASAP146_PD_NP21-04_PUT_2"
## [55] "AA_ASAP142_ctrl_NP22-37_PUT_3" "AA74_ASAP62_PD_NP16-140_PUT_3"
## [57] "AA_ASAP138_PD_NP16-285_PUT_3" "AA79_ASAP64_PD_NP16-162_PUT_3"
## [59] "AA_ASAP100_ctrl_NP18-148_PUT_3" "AA_ASAP93_ctrl_NP16-293_PUT_3"
## [61] "AA_ASAP139_PD_NP17-232_PUT_3" "AA89_ASAP78_ctrl_NP19-37_PUT_3"
## [63] "AA_ASAP149_PD_NP23-21_PUT_3" "AA86_ASAP73_PD_NP19-108_PUT_3"
## [65] "AA76_ASAP74_PD_NP19-255_PUT_3" "AA82_ASAP68_PD_NP18-117_PUT_3"
## [67] "AA_ASAP88_PD_NP21-217_PUT_3" "AA88_ASAP77_ctrl_NP19-36_PUT_3"
## [69] "AA85_ASAP72_PD_NP19-23_PUT_3" "AA83_ASAP69_PD_NP18-287_PUT_3"
## [71] "AA_ASAP87_PD_NP21-208_PUT_3" "AA_ASAP117_PD_NP22-55_PUT_3"
## [73] "AA_ASAP98_ctrl_NP16-119_PUT_3" "AA_ASAP96_ctrl_NP18-46_PUT_3"
## [75] "AA81_ASAP67_PD_NP17-191_PUT_3" "AA73_ASAP65_PD_NP16-269_PUT_3"
## [77] "AA_ASAP140_PD_NP19-91_PUT_3" "AA_ASAP141_ctrl_NP19-218_PUT_3"
## [79] "AA_ASAP144_PD_NP19-137_PUT_3" "AA84_ASAP71_PD_NP19-16_PUT_3"
## [81] "AA_ASAP97_PD_NP21-57_PUT_3" "AA87_ASAP76_ctrl_NP18-159_PUT_3"
## [83] "AA_ASAP146_PD_NP21-04_PUT_3" "AA71_ASAP70_PD_NP18-304_PUT_3"
## [85] "AA77_ASAP61_PD_NP16-25_PUT_3" "AA_ASAP94_ctrl_NP17-20_PUT_3"
## [87] "AA_ASAP92_ctrl_NP16-284_PUT_3" "AA_ASAP149_PD_NP23-21_PUT_5"
## [89] "AA78_ASAP63_PD_NP16-160_PUT_5" "AA_ASAP92_ctrl_NP16-284_PUT_5"
## [91] "AA_ASAP146_PD_NP21-04_PUT_5" "AA76_ASAP74_PD_NP19-255_PUT_5"
## [93] "AA82_ASAP68_PD_NP18-117_PUT_5" "AA_ASAP93_ctrl_NP16-293_PUT_5"
## [95] "AA85_ASAP72_PD_NP19-23_PUT_5" "AA_ASAP142_ctrl_NP22-37_PUT_5"
## [97] "AA73_ASAP65_PD_NP16-269_PUT_5" "AA89_ASAP78_ctrl_NP19-37_PUT_5"
## [99] "AA_ASAP94_ctrl_NP17-20_PUT_5" "AA86_ASAP73_PD_NP19-108_PUT_5"
## [101] "AA_ASAP96_ctrl_NP18-46_PUT_5" "AA_ASAP117_PD_NP22-55_PUT_5"
## [103] "AA79_ASAP64_PD_NP16-162_PUT_5" "AA71_ASAP70_PD_NP18-304_PUT_5"
## [105] "AA_ASAP139_PD_NP17-232_PUT_5" "AA_ASAP138_PD_NP16-285_PUT_5"
## [107] "AA_ASAP141_ctrl_NP19-218_PUT_5" "AA87_ASAP76_ctrl_NP18-159_PUT_5"
## [109] "AA_ASAP100_ctrl_NP18-148_PUT_5" "AA_ASAP97_PD_NP21-57_PUT_5"
## [111] "AA_ASAP87_PD_NP21-208_PUT_5" "AA84_ASAP71_PD_NP19-16_PUT_5"
## [113] "AA_ASAP88_PD_NP21-217_PUT_5" "AA88_ASAP77_ctrl_NP19-36_PUT_5"
## [115] "AA_ASAP98_ctrl_NP16-119_PUT_5" "AA74_ASAP62_PD_NP16-140_PUT_5"
## [117] "AA83_ASAP69_PD_NP18-287_PUT_5" "AA81_ASAP67_PD_NP17-191_PUT_5"
## [119] "AA77_ASAP61_PD_NP16-25_PUT_5" "AA_ASAP144_PD_NP19-137_PUT_5"
## [121] "AA_ASAP140_PD_NP19-91_PUT_5" "AA73_ASAP65_PD_NP16-269_PUT_4"
## [123] "AA_ASAP88_PD_NP21-217_PUT_4" "AA_ASAP140_PD_NP19-91_PUT_4"
## [125] "AA_ASAP96_ctrl_NP18-46_PUT_4" "AA85_ASAP72_PD_NP19-23_PUT_4"
## [127] "AA_ASAP87_PD_NP21-208_PUT_4" "AA_ASAP98_ctrl_NP16-119_PUT_4"
## [129] "AA_ASAP117_PD_NP22-55_PUT_4" "AA89_ASAP78_ctrl_NP19-37_PUT_4"
## [131] "AA_ASAP94_ctrl_NP17-20_PUT_4" "AA_ASAP138_PD_NP16-285_PUT_4"
## [133] "AA_ASAP141_ctrl_NP19-218_PUT_4" "AA76_ASAP74_PD_NP19-255_PUT_4"
## [135] "AA83_ASAP69_PD_NP18-287_PUT_4" "AA71_ASAP70_PD_NP18-304_PUT_4"
## [137] "AA84_ASAP71_PD_NP19-16_PUT_4" "AA_ASAP144_PD_NP19-137_PUT_4"
## [139] "AA79_ASAP64_PD_NP16-162_PUT_4" "AA87_ASAP76_ctrl_NP18-159_PUT_4"
## [141] "AA_ASAP100_ctrl_NP18-148_PUT_4" "AA_ASAP97_PD_NP21-57_PUT_4"
## [143] "AA77_ASAP61_PD_NP16-25_PUT_4" "AA81_ASAP67_PD_NP17-191_PUT_4"
## [145] "AA74_ASAP62_PD_NP16-140_PUT_4"
##
## $order_rows
## [1] "HERV_dup773" "HERV_dup1758" "HERV_dup1708" "HERV_dup3252" "HERV_dup1"
## [6] "HERV_dup288" "HERV_dup152" "HERV_dup2491" "HERV_dup3390" "HERV_dup631"
## [11] "HERV_dup2856" "HERV_dup2841" "HERV_dup1079" "HERV_dup600" "HERV_dup3357"
## [16] "HERV_dup1209" "HERV_dup1050" "HERV_dup2966" "HERV_dup302" "HERV_dup1000"
## [21] "HERV_dup265" "HERV_dup1702" "HERV_dup2838" "HERV_dup831" "HERV_dup54"
## [26] "HERV_dup1281" "HERV_dup2880" "HERV_dup470" "HERV_dup1283" "HERV_dup2900"
## [31] "HERV_dup1456" "HERV_dup2381" "HERV_dup93" "HERV_dup2273" "HERV_dup799"
## [36] "HERV_dup1669" "HERV_dup1888" "HERV_dup1102" "HERV_dup209" "HERV_dup1357"
## [41] "HERV_dup3266" "HERV_dup2789" "HERV_dup940" "HERV_dup1339" "HERV_dup980"
## [46] "HERV_dup384" "HERV_dup3226" "HERV_dup379" "HERV_dup1309" "HERV_dup1356"
## [51] "HERV_dup1308" "HERV_dup2365" "HERV_dup2550" "HERV_dup565" "HERV_dup2376"
## [56] "HERV_dup1598" "HERV_dup3423" "HERV_dup3174" "HERV_dup474" "HERV_dup1203"
## [61] "HERV_dup2879" "HERV_dup3105" "HERV_dup1657" "HERV_dup1701" "HERV_dup1004"
## [66] "HERV_dup518" "HERV_dup1002" "HERV_dup873" "HERV_dup1362" "HERV_dup112"
## [71] "HERV_dup2182" "HERV_dup151" "HERV_dup926" "HERV_dup1243" "HERV_dup2012"
## [76] "HERV_dup3363" "HERV_dup614" "HERV_dup1310" "HERV_dup1048" "HERV_dup3375"
## [81] "HERV_dup1670" "HERV_dup717" "HERV_dup1272" "HERV_dup3379" "HERV_dup562"
## [86] "HERV_dup37" "HERV_dup1052" "HERV_dup1449" "HERV_dup1319" "HERV_dup2106"
## [91] "HERV_dup731" "HERV_dup3343" "HERV_dup2941" "HERV_dup369" "HERV_dup880"
## [96] "HERV_dup3171" "HERV_dup1036" "HERV_dup1447" "HERV_dup1208" "HERV_dup1663"
## [101] "HERV_dup612" "HERV_dup597" "HERV_dup966" "HERV_dup417" "HERV_dup1315"
## [106] "HERV_dup904" "HERV_dup1371" "HERV_dup1359" "HERV_dup1255" "HERV_dup2176"
## [111] "HERV_dup292" "HERV_dup1667" "HERV_dup2530" "HERV_dup2599" "HERV_dup3355"
## [116] "HERV_dup380" "HERV_dup3196" "HERV_dup1382" "HERV_dup1334" "HERV_dup57"
## [121] "HERV_dup979" "HERV_dup2292" "HERV_dup3107" "HERV_dup1232" "HERV_dup2631"
## [126] "HERV_dup2843" "HERV_dup1351" "HERV_dup2847" "HERV_dup2589" "HERV_dup2914"
## [131] "HERV_dup301" "HERV_dup293" "HERV_dup1282" "HERV_dup758" "HERV_dup2261"
## [136] "HERV_dup1512" "HERV_dup3522" "HERV_dup1273" "HERV_dup899" "HERV_dup1755"
## [141] "HERV_dup2217" "HERV_dup1345" "HERV_dup1750" "HERV_dup954" "HERV_dup913"
## [146] "HERV_dup1940" "HERV_dup348" "HERV_dup1776" "HERV_dup3529" "HERV_dup1596"
## [151] "HERV_dup1001" "HERV_dup1749" "HERV_dup3140" "HERV_dup2438" "HERV_dup1934"
## [156] "HERV_dup2784" "HERV_dup2785" "HERV_dup3694" "HERV_dup1661" "HERV_dup1384"
## [161] "HERV_dup916" "HERV_dup5" "HERV_dup26" "HERV_dup1081" "HERV_dup1107"
## [166] "HERV_dup2752" "HERV_dup1269" "HERV_dup2964" "HERV_dup1694" "HERV_dup1303"
## [171] "HERV_dup1846" "HERV_dup939" "HERV_dup2963" "HERV_dup1112" "HERV_dup670"
## [176] "HERV_dup2250" "HERV_dup3050" "HERV_dup3580" "HERV_dup2422" "HERV_dup949"
## [181] "HERV_dup3418" "HERV_dup2111" "HERV_dup1007" "HERV_dup409" "HERV_dup355"
## [186] "HERV_dup2235" "HERV_dup110" "HERV_dup3417" "HERV_dup1307" "HERV_dup1875"
## [191] "HERV_dup2166" "HERV_dup2299" "HERV_dup1358" "HERV_dup3358" "HERV_dup2353"
## [196] "HERV_dup2266" "HERV_dup2412" "HERV_dup1780" "HERV_dup1847" "HERV_dup2643"
## [201] "HERV_dup3505" "HERV_dup3198" "HERV_dup2840" "HERV_dup2662" "HERV_dup468"
## [206] "HERV_dup487" "HERV_dup36" "HERV_dup482" "HERV_dup2603" "HERV_dup1611"
## [211] "HERV_dup1071" "HERV_dup2961" "HERV_dup2034" "HERV_dup969" "HERV_dup94"
## [216] "HERV_dup2801" "HERV_dup1662" "HERV_dup1920" "HERV_dup3033" "HERV_dup1046"
## [221] "HERV_dup2623" "HERV_dup2733" "HERV_dup203" "HERV_dup990" "HERV_dup118"
## [226] "HERV_dup1569" "HERV_dup554" "HERV_dup1613" "HERV_dup329" "HERV_dup2481"
## [231] "HERV_dup956" "HERV_dup133" "HERV_dup2566" "HERV_dup3124" "HERV_dup3108"
## [236] "HERV_dup18" "HERV_dup2803" "HERV_dup1756" "HERV_dup1717" "HERV_dup1703"
## [241] "HERV_dup872" "HERV_dup29" "HERV_dup58" "HERV_dup930" "HERV_dup1851"
## [246] "HERV_dup2646" "HERV_dup1184" "HERV_dup2719" "HERV_dup400" "HERV_dup433"
## [251] "HERV_dup1416" "HERV_dup586" "HERV_dup3341" "HERV_dup202" "HERV_dup1017"
## [256] "HERV_dup1316" "HERV_dup2482" "HERV_dup661" "HERV_dup2604" "HERV_dup2383"
## [261] "HERV_dup86" "HERV_dup2743" "HERV_dup968" "HERV_dup2163" "HERV_dup290"
## [266] "HERV_dup1707" "HERV_dup1240" "HERV_dup240" "HERV_dup471" "HERV_dup65"
## [271] "HERV_dup1253" "HERV_dup282" "HERV_dup1653" "HERV_dup1935" "HERV_dup2192"
## [276] "HERV_dup2834" "HERV_dup682" "HERV_dup2877" "HERV_dup732" "HERV_dup573"
## [281] "HERV_dup34" "HERV_dup1236" "HERV_dup2112" "HERV_dup1932" "HERV_dup3406"
## [286] "HERV_dup2158" "HERV_dup2905" "HERV_dup1302" "HERV_dup2588" "HERV_dup2857"
## [291] "HERV_dup2939" "HERV_dup2937" "HERV_dup2085" "HERV_dup1931" "HERV_dup2264"
## [296] "HERV_dup1317" "HERV_dup3020" "HERV_dup214" "HERV_dup2769" "HERV_dup3270"
## [301] "HERV_dup3519" "HERV_dup249" "HERV_dup300" "HERV_dup1374" "HERV_dup1605"
## [306] "HERV_dup2476" "HERV_dup398" "HERV_dup2736" "HERV_dup1089" "HERV_dup356"
## [311] "HERV_dup3251" "HERV_dup243" "HERV_dup1389" "HERV_dup3187" "HERV_dup1484"
## [316] "HERV_dup1187" "HERV_dup1982" "HERV_dup2093" "HERV_dup2878" "HERV_dup613"
## [321] "HERV_dup1730" "HERV_dup1541" "HERV_dup2500" "HERV_dup1752" "HERV_dup108"
## [326] "HERV_dup321" "HERV_dup3365" "HERV_dup3507" "HERV_dup2598" "HERV_dup1201"
## [331] "HERV_dup2902" "HERV_dup3148" "HERV_dup2524" "HERV_dup1890" "HERV_dup1195"
## [336] "HERV_dup1917" "HERV_dup2533" "HERV_dup218" "HERV_dup388" "HERV_dup1889"
## [341] "HERV_dup1304" "HERV_dup777" "HERV_dup492" "HERV_dup3063" "HERV_dup1973"
## [346] "HERV_dup1658" "HERV_dup2129" "HERV_dup1295" "HERV_dup1923" "HERV_dup1943"
## [351] "HERV_dup2562" "HERV_dup728" "HERV_dup626" "HERV_dup1324" "HERV_dup3545"
## [356] "HERV_dup2607" "HERV_dup890" "HERV_dup1802" "HERV_dup1073" "HERV_dup1182"
## [361] "HERV_dup3388" "HERV_dup1156" "HERV_dup1438" "HERV_dup2778" "HERV_dup882"
## [366] "HERV_dup3408" "HERV_dup2303" "HERV_dup180" "HERV_dup1298" "HERV_dup1285"
## [371] "HERV_dup3410" "HERV_dup1108" "HERV_dup1242" "HERV_dup467" "HERV_dup3210"
## [376] "HERV_dup3181" "HERV_dup2188" "HERV_dup1731" "HERV_dup1719" "HERV_dup2735"
## [381] "HERV_dup2942" "HERV_dup803" "HERV_dup3430" "HERV_dup1331" "HERV_dup1557"
## [386] "HERV_dup1972" "HERV_dup1005" "HERV_dup344" "HERV_dup1390" "HERV_dup3328"
## [391] "HERV_dup2187" "HERV_dup277" "HERV_dup3342" "HERV_dup1394" "HERV_dup441"
## [396] "HERV_dup2696" "HERV_dup2695" "HERV_dup1869" "HERV_dup1948" "HERV_dup272"
## [401] "HERV_dup2480" "HERV_dup331" "HERV_dup735" "HERV_dup599" "HERV_dup3227"
## [406] "HERV_dup1378" "HERV_dup1321" "HERV_dup3179" "HERV_dup2379" "HERV_dup1953"
## [411] "HERV_dup2936" "HERV_dup909" "HERV_dup1278" "HERV_dup2962" "HERV_dup1268"
## [416] "HERV_dup2179" "HERV_dup1617" "HERV_dup2812" "HERV_dup1629" "HERV_dup1437"
## [421] "HERV_dup61" "HERV_dup2891" "HERV_dup399" "HERV_dup3143" "HERV_dup443"
## [426] "HERV_dup215" "HERV_dup3220" "HERV_dup2159" "HERV_dup1210" "HERV_dup1433"
## [431] "HERV_dup928" "HERV_dup3351" "HERV_dup1453" "HERV_dup2561" "HERV_dup2739"
## [436] "HERV_dup2404" "HERV_dup3394" "HERV_dup3607" "HERV_dup27" "HERV_dup2391"
## [441] "HERV_dup2949" "HERV_dup127" "HERV_dup729" "HERV_dup3287" "HERV_dup572"
## [446] "HERV_dup723" "HERV_dup2797" "HERV_dup1297" "HERV_dup78" "HERV_dup2290"
## [451] "HERV_dup1333" "HERV_dup386" "HERV_dup2324" "HERV_dup530" "HERV_dup1440"
## [456] "HERV_dup2907" "HERV_dup2152" "HERV_dup1412" "HERV_dup1587" "HERV_dup1914"
## [461] "HERV_dup3286" "HERV_dup772" "HERV_dup2635" "HERV_dup3013" "HERV_dup517"
## [466] "HERV_dup1218" "HERV_dup736" "HERV_dup2896" "HERV_dup3100" "HERV_dup2278"
## [471] "HERV_dup3688" "HERV_dup1254" "HERV_dup3137" "HERV_dup2663" "HERV_dup201"
## [476] "HERV_dup1213" "HERV_dup3366" "HERV_dup3319" "HERV_dup2536" "HERV_dup2134"
## [481] "HERV_dup662" "HERV_dup1222" "HERV_dup1500" "HERV_dup3217" "HERV_dup2967"
## [486] "HERV_dup1129" "HERV_dup377" "HERV_dup1114" "HERV_dup894" "HERV_dup3231"
## [491] "HERV_dup1350" "HERV_dup2141" "HERV_dup852" "HERV_dup1640" "HERV_dup2320"
## [496] "HERV_dup2298" "HERV_dup2855" "HERV_dup2378" "HERV_dup1248" "HERV_dup3239"
## [501] "HERV_dup469" "HERV_dup3606" "HERV_dup1029" "HERV_dup1804" "HERV_dup129"
## [506] "HERV_dup2518" "HERV_dup2706" "HERV_dup2804" "HERV_dup1381" "HERV_dup21"
## [511] "HERV_dup2183" "HERV_dup1579" "HERV_dup876" "HERV_dup2897" "HERV_dup2130"
## [516] "HERV_dup1366" "HERV_dup2282" "HERV_dup870" "HERV_dup2041" "HERV_dup1090"
## [521] "HERV_dup1279" "HERV_dup1470" "HERV_dup184" "HERV_dup2033" "HERV_dup1757"
## [526] "HERV_dup2356" "HERV_dup553" "HERV_dup927" "HERV_dup2647" "HERV_dup1526"
## [531] "HERV_dup1103" "HERV_dup1720" "HERV_dup900" "HERV_dup2019" "HERV_dup851"
## [536] "HERV_dup1556" "HERV_dup17" "HERV_dup251" "HERV_dup1082" "HERV_dup2436"
## [541] "HERV_dup2728" "HERV_dup933" "HERV_dup2915" "HERV_dup419" "HERV_dup3481"
## [546] "HERV_dup1671" "HERV_dup1080" "HERV_dup115" "HERV_dup3118" "HERV_dup2886"
## [551] "HERV_dup3416" "HERV_dup632" "HERV_dup1212" "HERV_dup1047" "HERV_dup3248"
## [556] "HERV_dup2934" "HERV_dup488" "HERV_dup703" "HERV_dup710" "HERV_dup935"
## [561] "HERV_dup1868" "HERV_dup3215" "HERV_dup3673" "HERV_dup924" "HERV_dup2747"
## [566] "HERV_dup1724" "HERV_dup120" "HERV_dup577" "HERV_dup1979" "HERV_dup1413"
## [571] "HERV_dup934" "HERV_dup407" "HERV_dup1383" "HERV_dup2529" "HERV_dup568"
## [576] "HERV_dup982" "HERV_dup2002" "HERV_dup2848" "HERV_dup2100" "HERV_dup2557"
## [581] "HERV_dup357" "HERV_dup2809" "HERV_dup23" "HERV_dup3212" "HERV_dup2823"
## [586] "HERV_dup1891" "HERV_dup1235" "HERV_dup1014" "HERV_dup2548" "HERV_dup967"
## [591] "HERV_dup1962" "HERV_dup1926" "HERV_dup846" "HERV_dup434" "HERV_dup519"
## [596] "HERV_dup1093" "HERV_dup2977" "HERV_dup2149" "HERV_dup975" "HERV_dup776"
## [601] "HERV_dup38" "HERV_dup3182" "HERV_dup665" "HERV_dup1937" "HERV_dup1668"
## [606] "HERV_dup1532" "HERV_dup2655" "HERV_dup2651" "HERV_dup3459" "HERV_dup1944"
## [611] "HERV_dup692" "HERV_dup1415" "HERV_dup1364" "HERV_dup1673" "HERV_dup2653"
## [616] "HERV_dup2319" "HERV_dup2555" "HERV_dup2945" "HERV_dup1064" "HERV_dup2334"
## [621] "HERV_dup3219" "HERV_dup2242" "HERV_dup1245" "HERV_dup2620" "HERV_dup2985"
## [626] "HERV_dup2979" "HERV_dup3131" "HERV_dup739" "HERV_dup3008" "HERV_dup556"
## [631] "HERV_dup1131" "HERV_dup591" "HERV_dup3037" "HERV_dup2525" "HERV_dup1038"
## [636] "HERV_dup2366" "HERV_dup250" "HERV_dup2027" "HERV_dup595" "HERV_dup1614"
## [641] "HERV_dup2415" "HERV_dup1049" "HERV_dup1555" "HERV_dup314" "HERV_dup1239"
## [646] "HERV_dup276" "HERV_dup3588" "HERV_dup884" "HERV_dup1228" "HERV_dup1403"
## [651] "HERV_dup194" "HERV_dup1401" "HERV_dup1778" "HERV_dup1099" "HERV_dup1013"
## [656] "HERV_dup1902" "HERV_dup183" "HERV_dup3117" "HERV_dup2632" "HERV_dup2272"
## [661] "HERV_dup1513" "HERV_dup634" "HERV_dup2137" "HERV_dup2464" "HERV_dup173"
## [666] "HERV_dup3189" "HERV_dup336" "HERV_dup39" "HERV_dup1655" "HERV_dup350"
## [671] "HERV_dup3284" "HERV_dup2337" "HERV_dup177" "HERV_dup2128" "HERV_dup291"
## [676] "HERV_dup640" "HERV_dup446" "HERV_dup551" "HERV_dup3031" "HERV_dup724"
## [681] "HERV_dup850" "HERV_dup1494" "HERV_dup1933" "HERV_dup1327" "HERV_dup185"
## [686] "HERV_dup1639" "HERV_dup1496" "HERV_dup1322" "HERV_dup570" "HERV_dup3044"
## [691] "HERV_dup2894" "HERV_dup746" "HERV_dup1656" "HERV_dup981" "HERV_dup1733"
## [696] "HERV_dup977" "HERV_dup3073" "HERV_dup505" "HERV_dup578" "HERV_dup1872"
## [701] "HERV_dup447" "HERV_dup1527" "HERV_dup1146" "HERV_dup389" "HERV_dup508"
## [706] "HERV_dup2978" "HERV_dup1549" "HERV_dup2441" "HERV_dup3335" "HERV_dup1664"
## [711] "HERV_dup2772" "HERV_dup1823" "HERV_dup2602" "HERV_dup461" "HERV_dup450"
## [716] "HERV_dup671" "HERV_dup1958" "HERV_dup509" "HERV_dup1491" "HERV_dup3015"
## [721] "HERV_dup3154" "HERV_dup1520" "HERV_dup1346" "HERV_dup1638" "HERV_dup1172"
## [726] "HERV_dup1514" "HERV_dup2479" "HERV_dup452" "HERV_dup2875" "HERV_dup2730"
## [731] "HERV_dup1459" "HERV_dup84" "HERV_dup1711" "HERV_dup2680" "HERV_dup2972"
## [736] "HERV_dup1417" "HERV_dup381" "HERV_dup1003" "HERV_dup3016"
asap_heatmap_snRNA(region = c("AMY"),
tes = data_TE_annotation[which(data_TE_annotation$type == "HERV"),"TE_id"],
return_df = F,
breaks = seq(0,15,length.out = 52),
data = TE_data,
group_cols = c("celltype"),
index_row_reorder = c(HERVs_sorted_amy),
order_cols_groups = order_cols_celltype,
title = "AMY HERV: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
annotation_cols = annotation_cols)

## $heatmap
##
## $order_cols
## [1] "AA_ASAP114_PD_NP21-57_AMY_0" "DA811_ASAP18_PD_NP16-140_AMY_0"
## [3] "DA802_ASAP40_PD_NP19-23_AMY_0" "DA780_ASAP37_PD_NP19-16_AMY_0"
## [5] "AA_ASAP110_ctrl_NP16-119_AMY_0" "AA_ASAP115_PD_NP21-208_AMY_0"
## [7] "DA783_ASAP45_PD_NP19-255_AMY_0" "DA474_ASAP24_PD_NP16-25_AMY_0"
## [9] "DA778_ASAP31_PD_NP18-117_AMY_0" "DA791_ASAP50_ctrl_NP18-159_AMY_0"
## [11] "DA793_ASAP53_ctrl_NP19-36_AMY_0" "DA805_ASAP56_ctrl_NP19-37_AMY_0"
## [13] "AA_ASAP123_ctrl_NP19-218_AMY_1" "AA_ASAP114_PD_NP21-57_AMY_1"
## [15] "AA_ASAP113_ctrl_NP18-148_AMY_1" "AA_ASAP126_PD_NP19-137_AMY_1"
## [17] "AA_ASAP115_PD_NP21-208_AMY_1" "AA_ASAP110_ctrl_NP16-119_AMY_1"
## [19] "DA512_ASAP60_ctrl_NP19-45_AMY_1" "AA_ASAP124_ctrl_NP22-37_AMY_1"
## [21] "AA_ASAP119_PD_NP22-55_AMY_1" "AA_ASAP121_PD_NP17-232_AMY_1"
## [23] "AA_ASAP128_PD_NP21-04_AMY_1" "AA_ASAP131_PD_NP23-21_AMY_1"
## [25] "AA_ASAP109_PD_NP21-217_AMY_1" "DA811_ASAP18_PD_NP16-140_AMY_1"
## [27] "DA793_ASAP53_ctrl_NP19-36_AMY_1" "DA783_ASAP45_PD_NP19-255_AMY_1"
## [29] "DA474_ASAP24_PD_NP16-25_AMY_1" "DA791_ASAP50_ctrl_NP18-159_AMY_1"
## [31] "DA778_ASAP31_PD_NP18-117_AMY_1" "DA805_ASAP56_ctrl_NP19-37_AMY_1"
## [33] "DA802_ASAP40_PD_NP19-23_AMY_1" "DA801_ASAP53_ctrl_NP19-36_AMY_1"
## [35] "DA780_ASAP37_PD_NP19-16_AMY_1" "ASAP122_PD_NP19-91_AMY_2"
## [37] "AA_ASAP128_PD_NP21-04_AMY_2" "AA_ASAP120_PD_NP16-285_AMY_2"
## [39] "AA_ASAP119_PD_NP22-55_AMY_2" "AA_ASAP109_PD_NP21-217_AMY_2"
## [41] "AA_ASAP126_PD_NP19-137_AMY_2" "AA_ASAP131_PD_NP23-21_AMY_2"
## [43] "DA814_ASAP35_PD_NP18-304_AMY_2" "DA801_ASAP53_ctrl_NP19-36_AMY_2"
## [45] "DA778_ASAP31_PD_NP18-117_AMY_2" "DA793_ASAP53_ctrl_NP19-36_AMY_2"
## [47] "AA_ASAP110_ctrl_NP16-119_AMY_2" "AA_ASAP114_PD_NP21-57_AMY_2"
## [49] "AA_ASAP123_ctrl_NP19-218_AMY_2" "DA805_ASAP56_ctrl_NP19-37_AMY_2"
## [51] "AA_ASAP121_PD_NP17-232_AMY_2" "DA811_ASAP18_PD_NP16-140_AMY_2"
## [53] "AA_ASAP112_ctrl_NP16-293_AMY_2" "DA512_ASAP60_ctrl_NP19-45_AMY_2"
## [55] "AA_ASAP113_ctrl_NP18-148_AMY_2" "DA807_ASAP29_PD_NP17-191_AMY_2"
## [57] "DA474_ASAP24_PD_NP16-25_AMY_2" "AA_ASAP115_PD_NP21-208_AMY_2"
## [59] "DA783_ASAP45_PD_NP19-255_AMY_2" "DA791_ASAP50_ctrl_NP18-159_AMY_2"
## [61] "DA802_ASAP40_PD_NP19-23_AMY_2" "AA_ASAP124_ctrl_NP22-37_AMY_2"
## [63] "DA780_ASAP37_PD_NP19-16_AMY_2" "DA811_ASAP18_PD_NP16-140_AMY_3"
## [65] "AA_ASAP119_PD_NP22-55_AMY_3" "AA_ASAP121_PD_NP17-232_AMY_3"
## [67] "AA_ASAP109_PD_NP21-217_AMY_3" "DA802_ASAP40_PD_NP19-23_AMY_3"
## [69] "AA_ASAP111_ctrl_NP16-284_AMY_3" "DA803_ASAP48_ctrl_NP17-256_AMY_3"
## [71] "AA_ASAP120_PD_NP16-285_AMY_3" "ASAP122_PD_NP19-91_AMY_3"
## [73] "AA_ASAP115_PD_NP21-208_AMY_3" "DA783_ASAP45_PD_NP19-255_AMY_3"
## [75] "AA_ASAP112_ctrl_NP16-293_AMY_3" "AA_ASAP131_PD_NP23-21_AMY_3"
## [77] "DA780_ASAP37_PD_NP19-16_AMY_3" "AA_ASAP114_PD_NP21-57_AMY_3"
## [79] "DA778_ASAP31_PD_NP18-117_AMY_3" "DA791_ASAP50_ctrl_NP18-159_AMY_3"
## [81] "DA793_ASAP53_ctrl_NP19-36_AMY_3" "DA801_ASAP53_ctrl_NP19-36_AMY_3"
## [83] "DA807_ASAP29_PD_NP17-191_AMY_3" "DA474_ASAP24_PD_NP16-25_AMY_3"
## [85] "AA_ASAP110_ctrl_NP16-119_AMY_3" "DA805_ASAP56_ctrl_NP19-37_AMY_3"
## [87] "AA_ASAP124_ctrl_NP22-37_AMY_3" "AA_ASAP128_PD_NP21-04_AMY_3"
## [89] "AA_ASAP123_ctrl_NP19-218_AMY_3" "DA512_ASAP60_ctrl_NP19-45_AMY_3"
## [91] "AA_ASAP113_ctrl_NP18-148_AMY_3" "DA778_ASAP31_PD_NP18-117_AMY_5"
## [93] "AA_ASAP131_PD_NP23-21_AMY_5" "DA800_ASAP20_PD_NP16-160_AMY_5"
## [95] "AA_ASAP114_PD_NP21-57_AMY_5" "AA_ASAP113_ctrl_NP18-148_AMY_5"
## [97] "ASAP122_PD_NP19-91_AMY_5" "DA791_ASAP50_ctrl_NP18-159_AMY_5"
## [99] "DA793_ASAP53_ctrl_NP19-36_AMY_5" "DA474_ASAP24_PD_NP16-25_AMY_5"
## [101] "DA805_ASAP56_ctrl_NP19-37_AMY_5" "AA_ASAP109_PD_NP21-217_AMY_5"
## [103] "DA802_ASAP40_PD_NP19-23_AMY_5" "AA_ASAP121_PD_NP17-232_AMY_5"
## [105] "AA_ASAP124_ctrl_NP22-37_AMY_5" "DA811_ASAP18_PD_NP16-140_AMY_5"
## [107] "DA814_ASAP35_PD_NP18-304_AMY_5" "DA779_ASAP33_PD_NP18-287_AMY_5"
## [109] "AA_ASAP115_PD_NP21-208_AMY_5" "AA_ASAP126_PD_NP19-137_AMY_5"
## [111] "DA512_ASAP60_ctrl_NP19-45_AMY_5" "AA_ASAP110_ctrl_NP16-119_AMY_5"
## [113] "DA783_ASAP45_PD_NP19-255_AMY_5" "DA803_ASAP48_ctrl_NP17-256_AMY_5"
## [115] "AA_ASAP120_PD_NP16-285_AMY_5" "DA807_ASAP29_PD_NP17-191_AMY_5"
## [117] "DA780_ASAP37_PD_NP19-16_AMY_5" "DA801_ASAP53_ctrl_NP19-36_AMY_5"
## [119] "AA_ASAP123_ctrl_NP19-218_AMY_5" "AA_ASAP112_ctrl_NP16-293_AMY_5"
## [121] "AA_ASAP119_PD_NP22-55_AMY_5" "AA_ASAP128_PD_NP21-04_AMY_5"
## [123] "DA815_ASAP37_PD_NP19-16_AMY_5" "DA802_ASAP40_PD_NP19-23_AMY_4"
## [125] "AA_ASAP112_ctrl_NP16-293_AMY_4" "DA512_ASAP60_ctrl_NP19-45_AMY_4"
## [127] "AA_ASAP126_PD_NP19-137_AMY_4" "AA_ASAP115_PD_NP21-208_AMY_4"
## [129] "AA_ASAP131_PD_NP23-21_AMY_4" "DA783_ASAP45_PD_NP19-255_AMY_4"
## [131] "DA811_ASAP18_PD_NP16-140_AMY_4" "DA805_ASAP56_ctrl_NP19-37_AMY_4"
## [133] "DA474_ASAP24_PD_NP16-25_AMY_4" "AA_ASAP119_PD_NP22-55_AMY_4"
## [135] "DA801_ASAP53_ctrl_NP19-36_AMY_4" "DA793_ASAP53_ctrl_NP19-36_AMY_4"
## [137] "AA_ASAP110_ctrl_NP16-119_AMY_4" "DA791_ASAP50_ctrl_NP18-159_AMY_4"
## [139] "DA807_ASAP29_PD_NP17-191_AMY_4" "DA778_ASAP31_PD_NP18-117_AMY_4"
## [141] "AA_ASAP114_PD_NP21-57_AMY_4" "AA_ASAP123_ctrl_NP19-218_AMY_4"
## [143] "AA_ASAP113_ctrl_NP18-148_AMY_4" "AA_ASAP123_ctrl_NP19-218_AMY_6"
##
## $order_rows
## [1] "HERV_dup773" "HERV_dup1758" "HERV_dup288" "HERV_dup1" "HERV_dup3252"
## [6] "HERV_dup152" "HERV_dup2491" "HERV_dup1708" "HERV_dup3390" "HERV_dup2856"
## [11] "HERV_dup1281" "HERV_dup1209" "HERV_dup265" "HERV_dup600" "HERV_dup2966"
## [16] "HERV_dup302" "HERV_dup2841" "HERV_dup1079" "HERV_dup2838" "HERV_dup799"
## [21] "HERV_dup3357" "HERV_dup926" "HERV_dup1702" "HERV_dup1050" "HERV_dup614"
## [26] "HERV_dup2880" "HERV_dup1000" "HERV_dup631" "HERV_dup470" "HERV_dup3226"
## [31] "HERV_dup384" "HERV_dup2273" "HERV_dup54" "HERV_dup1283" "HERV_dup940"
## [36] "HERV_dup2900" "HERV_dup1456" "HERV_dup1669" "HERV_dup2381" "HERV_dup293"
## [41] "HERV_dup1339" "HERV_dup1888" "HERV_dup2789" "HERV_dup1357" "HERV_dup3266"
## [46] "HERV_dup379" "HERV_dup1359" "HERV_dup3171" "HERV_dup209" "HERV_dup2365"
## [51] "HERV_dup1102" "HERV_dup112" "HERV_dup1598" "HERV_dup980" "HERV_dup1356"
## [56] "HERV_dup93" "HERV_dup717" "HERV_dup417" "HERV_dup1657" "HERV_dup3363"
## [61] "HERV_dup3174" "HERV_dup2376" "HERV_dup3105" "HERV_dup1002" "HERV_dup3379"
## [66] "HERV_dup831" "HERV_dup3423" "HERV_dup1004" "HERV_dup562" "HERV_dup1309"
## [71] "HERV_dup2840" "HERV_dup474" "HERV_dup1308" "HERV_dup873" "HERV_dup2182"
## [76] "HERV_dup1203" "HERV_dup1310" "HERV_dup1701" "HERV_dup3343" "HERV_dup1667"
## [81] "HERV_dup916" "HERV_dup518" "HERV_dup904" "HERV_dup3375" "HERV_dup612"
## [86] "HERV_dup1382" "HERV_dup1362" "HERV_dup1319" "HERV_dup2012" "HERV_dup2299"
## [91] "HERV_dup1934" "HERV_dup1670" "HERV_dup670" "HERV_dup37" "HERV_dup1048"
## [96] "HERV_dup2106" "HERV_dup1255" "HERV_dup731" "HERV_dup1345" "HERV_dup2879"
## [101] "HERV_dup1449" "HERV_dup1315" "HERV_dup1334" "HERV_dup443" "HERV_dup1755"
## [106] "HERV_dup1052" "HERV_dup151" "HERV_dup3107" "HERV_dup1272" "HERV_dup1447"
## [111] "HERV_dup2217" "HERV_dup2292" "HERV_dup1694" "HERV_dup3522" "HERV_dup3355"
## [116] "HERV_dup966" "HERV_dup1282" "HERV_dup1307" "HERV_dup2176" "HERV_dup110"
## [121] "HERV_dup1512" "HERV_dup1371" "HERV_dup2843" "HERV_dup565" "HERV_dup1750"
## [126] "HERV_dup899" "HERV_dup1611" "HERV_dup301" "HERV_dup348" "HERV_dup1017"
## [131] "HERV_dup1208" "HERV_dup2914" "HERV_dup682" "HERV_dup913" "HERV_dup1846"
## [136] "HERV_dup2631" "HERV_dup292" "HERV_dup57" "HERV_dup872" "HERV_dup1663"
## [141] "HERV_dup482" "HERV_dup369" "HERV_dup758" "HERV_dup1001" "HERV_dup2530"
## [146] "HERV_dup2163" "HERV_dup2603" "HERV_dup1046" "HERV_dup3430" "HERV_dup880"
## [151] "HERV_dup597" "HERV_dup2902" "HERV_dup3140" "HERV_dup1875" "HERV_dup969"
## [156] "HERV_dup2261" "HERV_dup2550" "HERV_dup1596" "HERV_dup2438" "HERV_dup3417"
## [161] "HERV_dup1107" "HERV_dup939" "HERV_dup2599" "HERV_dup1613" "HERV_dup3505"
## [166] "HERV_dup1351" "HERV_dup1776" "HERV_dup3050" "HERV_dup26" "HERV_dup380"
## [171] "HERV_dup203" "HERV_dup1232" "HERV_dup1273" "HERV_dup1253" "HERV_dup2412"
## [176] "HERV_dup2589" "HERV_dup3418" "HERV_dup2847" "HERV_dup2111" "HERV_dup979"
## [181] "HERV_dup1662" "HERV_dup2963" "HERV_dup3529" "HERV_dup2235" "HERV_dup2961"
## [186] "HERV_dup2566" "HERV_dup1303" "HERV_dup2643" "HERV_dup2662" "HERV_dup5"
## [191] "HERV_dup2752" "HERV_dup954" "HERV_dup487" "HERV_dup18" "HERV_dup65"
## [196] "HERV_dup1243" "HERV_dup34" "HERV_dup2391" "HERV_dup1112" "HERV_dup1081"
## [201] "HERV_dup433" "HERV_dup1940" "HERV_dup2476" "HERV_dup1569" "HERV_dup468"
## [206] "HERV_dup1242" "HERV_dup3580" "HERV_dup956" "HERV_dup1703" "HERV_dup356"
## [211] "HERV_dup1269" "HERV_dup1358" "HERV_dup2719" "HERV_dup3196" "HERV_dup573"
## [216] "HERV_dup2166" "HERV_dup3694" "HERV_dup118" "HERV_dup290" "HERV_dup1416"
## [221] "HERV_dup3227" "HERV_dup1935" "HERV_dup1036" "HERV_dup1780" "HERV_dup355"
## [226] "HERV_dup949" "HERV_dup2266" "HERV_dup1302" "HERV_dup1661" "HERV_dup2857"
## [231] "HERV_dup94" "HERV_dup1717" "HERV_dup36" "HERV_dup2812" "HERV_dup3198"
## [236] "HERV_dup2784" "HERV_dup3033" "HERV_dup1331" "HERV_dup1007" "HERV_dup1605"
## [241] "HERV_dup1917" "HERV_dup2607" "HERV_dup2878" "HERV_dup218" "HERV_dup613"
## [246] "HERV_dup1500" "HERV_dup1213" "HERV_dup2183" "HERV_dup1749" "HERV_dup1847"
## [251] "HERV_dup2778" "HERV_dup1756" "HERV_dup471" "HERV_dup1932" "HERV_dup2834"
## [256] "HERV_dup1707" "HERV_dup2250" "HERV_dup3251" "HERV_dup3187" "HERV_dup2561"
## [261] "HERV_dup27" "HERV_dup329" "HERV_dup1555" "HERV_dup2366" "HERV_dup2112"
## [266] "HERV_dup1484" "HERV_dup1982" "HERV_dup2939" "HERV_dup202" "HERV_dup2623"
## [271] "HERV_dup3342" "HERV_dup927" "HERV_dup2422" "HERV_dup29" "HERV_dup1617"
## [276] "HERV_dup2823" "HERV_dup2085" "HERV_dup3358" "HERV_dup3270" "HERV_dup3063"
## [281] "HERV_dup2801" "HERV_dup2936" "HERV_dup282" "HERV_dup3013" "HERV_dup214"
## [286] "HERV_dup1073" "HERV_dup2769" "HERV_dup2877" "HERV_dup3143" "HERV_dup3020"
## [291] "HERV_dup990" "HERV_dup3406" "HERV_dup2941" "HERV_dup3124" "HERV_dup399"
## [296] "HERV_dup1720" "HERV_dup1730" "HERV_dup586" "HERV_dup108" "HERV_dup1268"
## [301] "HERV_dup2188" "HERV_dup1394" "HERV_dup2264" "HERV_dup1089" "HERV_dup2480"
## [306] "HERV_dup1298" "HERV_dup1920" "HERV_dup1240" "HERV_dup2353" "HERV_dup632"
## [311] "HERV_dup2736" "HERV_dup2964" "HERV_dup1071" "HERV_dup1802" "HERV_dup1297"
## [316] "HERV_dup1453" "HERV_dup554" "HERV_dup251" "HERV_dup1972" "HERV_dup120"
## [321] "HERV_dup1869" "HERV_dup314" "HERV_dup1316" "HERV_dup661" "HERV_dup1390"
## [326] "HERV_dup2319" "HERV_dup2598" "HERV_dup968" "HERV_dup2785" "HERV_dup1236"
## [331] "HERV_dup2915" "HERV_dup488" "HERV_dup1931" "HERV_dup2379" "HERV_dup3410"
## [336] "HERV_dup3365" "HERV_dup2695" "HERV_dup1731" "HERV_dup2093" "HERV_dup3408"
## [341] "HERV_dup3239" "HERV_dup1890" "HERV_dup2949" "HERV_dup1557" "HERV_dup2896"
## [346] "HERV_dup3319" "HERV_dup58" "HERV_dup890" "HERV_dup2436" "HERV_dup2803"
## [351] "HERV_dup2149" "HERV_dup3231" "HERV_dup2962" "HERV_dup746" "HERV_dup626"
## [356] "HERV_dup1324" "HERV_dup876" "HERV_dup1321" "HERV_dup2533" "HERV_dup2383"
## [361] "HERV_dup3507" "HERV_dup2415" "HERV_dup1295" "HERV_dup2129" "HERV_dup1437"
## [366] "HERV_dup350" "HERV_dup215" "HERV_dup3388" "HERV_dup662" "HERV_dup467"
## [371] "HERV_dup3341" "HERV_dup2733" "HERV_dup249" "HERV_dup517" "HERV_dup1494"
## [376] "HERV_dup1374" "HERV_dup1587" "HERV_dup3286" "HERV_dup3148" "HERV_dup409"
## [381] "HERV_dup377" "HERV_dup1556" "HERV_dup2588" "HERV_dup441" "HERV_dup967"
## [386] "HERV_dup2529" "HERV_dup729" "HERV_dup1973" "HERV_dup2735" "HERV_dup2646"
## [391] "HERV_dup1532" "HERV_dup2500" "HERV_dup2653" "HERV_dup2555" "HERV_dup386"
## [396] "HERV_dup2772" "HERV_dup3351" "HERV_dup2651" "HERV_dup982" "HERV_dup1187"
## [401] "HERV_dup1093" "HERV_dup2192" "HERV_dup1640" "HERV_dup1655" "HERV_dup1317"
## [406] "HERV_dup3366" "HERV_dup851" "HERV_dup1658" "HERV_dup3118" "HERV_dup3037"
## [411] "HERV_dup1228" "HERV_dup3220" "HERV_dup2739" "HERV_dup1851" "HERV_dup1953"
## [416] "HERV_dup2158" "HERV_dup3108" "HERV_dup665" "HERV_dup2242" "HERV_dup1005"
## [421] "HERV_dup2298" "HERV_dup2179" "HERV_dup777" "HERV_dup591" "HERV_dup599"
## [426] "HERV_dup3100" "HERV_dup2562" "HERV_dup180" "HERV_dup357" "HERV_dup1029"
## [431] "HERV_dup1653" "HERV_dup1491" "HERV_dup1671" "HERV_dup2696" "HERV_dup3416"
## [436] "HERV_dup23" "HERV_dup2905" "HERV_dup2886" "HERV_dup1080" "HERV_dup928"
## [441] "HERV_dup3217" "HERV_dup1719" "HERV_dup1433" "HERV_dup2481" "HERV_dup3328"
## [446] "HERV_dup577" "HERV_dup2747" "HERV_dup2977" "HERV_dup2848" "HERV_dup2604"
## [451] "HERV_dup331" "HERV_dup1366" "HERV_dup508" "HERV_dup2033" "HERV_dup710"
## [456] "HERV_dup2730" "HERV_dup1614" "HERV_dup934" "HERV_dup551" "HERV_dup469"
## [461] "HERV_dup115" "HERV_dup1210" "HERV_dup3212" "HERV_dup2272" "HERV_dup1389"
## [466] "HERV_dup1804" "HERV_dup2337" "HERV_dup1384" "HERV_dup492" "HERV_dup3394"
## [471] "HERV_dup1440" "HERV_dup1038" "HERV_dup1222" "HERV_dup1064" "HERV_dup419"
## [476] "HERV_dup2632" "HERV_dup2187" "HERV_dup2034" "HERV_dup1668" "HERV_dup1285"
## [481] "HERV_dup1520" "HERV_dup1156" "HERV_dup2620" "HERV_dup852" "HERV_dup1438"
## [486] "HERV_dup2891" "HERV_dup1889" "HERV_dup300" "HERV_dup900" "HERV_dup732"
## [491] "HERV_dup1937" "HERV_dup3044" "HERV_dup2978" "HERV_dup870" "HERV_dup38"
## [496] "HERV_dup1496" "HERV_dup1926" "HERV_dup2303" "HERV_dup1013" "HERV_dup1201"
## [501] "HERV_dup3673" "HERV_dup909" "HERV_dup1914" "HERV_dup894" "HERV_dup975"
## [506] "HERV_dup2655" "HERV_dup1923" "HERV_dup272" "HERV_dup723" "HERV_dup2027"
## [511] "HERV_dup739" "HERV_dup2130" "HERV_dup3248" "HERV_dup336" "HERV_dup2137"
## [516] "HERV_dup2680" "HERV_dup1047" "HERV_dup2282" "HERV_dup2706" "HERV_dup1513"
## [521] "HERV_dup2804" "HERV_dup2663" "HERV_dup2524" "HERV_dup173" "HERV_dup3335"
## [526] "HERV_dup127" "HERV_dup1724" "HERV_dup1212" "HERV_dup2041" "HERV_dup933"
## [531] "HERV_dup3459" "HERV_dup1350" "HERV_dup1278" "HERV_dup1381" "HERV_dup3008"
## [536] "HERV_dup194" "HERV_dup61" "HERV_dup1378" "HERV_dup2378" "HERV_dup388"
## [541] "HERV_dup250" "HERV_dup2647" "HERV_dup344" "HERV_dup3688" "HERV_dup1304"
## [546] "HERV_dup1090" "HERV_dup1114" "HERV_dup3215" "HERV_dup1891" "HERV_dup519"
## [551] "HERV_dup553" "HERV_dup2019" "HERV_dup243" "HERV_dup184" "HERV_dup2934"
## [556] "HERV_dup1541" "HERV_dup2536" "HERV_dup2128" "HERV_dup3117" "HERV_dup2404"
## [561] "HERV_dup1962" "HERV_dup977" "HERV_dup1103" "HERV_dup3284" "HERV_dup3481"
## [566] "HERV_dup2141" "HERV_dup2809" "HERV_dup1979" "HERV_dup277" "HERV_dup461"
## [571] "HERV_dup3210" "HERV_dup1279" "HERV_dup884" "HERV_dup1235" "HERV_dup39"
## [576] "HERV_dup1412" "HERV_dup736" "HERV_dup1948" "HERV_dup935" "HERV_dup434"
## [581] "HERV_dup2985" "HERV_dup882" "HERV_dup2797" "HERV_dup570" "HERV_dup2635"
## [586] "HERV_dup1579" "HERV_dup3131" "HERV_dup2002" "HERV_dup1902" "HERV_dup1195"
## [591] "HERV_dup1248" "HERV_dup1218" "HERV_dup803" "HERV_dup724" "HERV_dup2278"
## [596] "HERV_dup2937" "HERV_dup578" "HERV_dup1383" "HERV_dup276" "HERV_dup2134"
## [601] "HERV_dup1129" "HERV_dup1527" "HERV_dup556" "HERV_dup2907" "HERV_dup3519"
## [606] "HERV_dup2548" "HERV_dup2855" "HERV_dup1082" "HERV_dup1049" "HERV_dup1526"
## [611] "HERV_dup505" "HERV_dup321" "HERV_dup1470" "HERV_dup2728" "HERV_dup86"
## [616] "HERV_dup1778" "HERV_dup21" "HERV_dup1413" "HERV_dup2100" "HERV_dup568"
## [621] "HERV_dup1638" "HERV_dup2334" "HERV_dup1364" "HERV_dup530" "HERV_dup1629"
## [626] "HERV_dup1333" "HERV_dup1254" "HERV_dup2602" "HERV_dup84" "HERV_dup1245"
## [631] "HERV_dup776" "HERV_dup1417" "HERV_dup1401" "HERV_dup2290" "HERV_dup2320"
## [636] "HERV_dup3031" "HERV_dup3179" "HERV_dup692" "HERV_dup3287" "HERV_dup2152"
## [641] "HERV_dup2979" "HERV_dup572" "HERV_dup1944" "HERV_dup3182" "HERV_dup2159"
## [646] "HERV_dup185" "HERV_dup3073" "HERV_dup728" "HERV_dup1014" "HERV_dup1757"
## [651] "HERV_dup735" "HERV_dup1108" "HERV_dup671" "HERV_dup407" "HERV_dup240"
## [656] "HERV_dup17" "HERV_dup291" "HERV_dup201" "HERV_dup1933" "HERV_dup595"
## [661] "HERV_dup703" "HERV_dup2518" "HERV_dup1184" "HERV_dup1182" "HERV_dup1872"
## [666] "HERV_dup446" "HERV_dup1664" "HERV_dup1711" "HERV_dup1131" "HERV_dup2482"
## [671] "HERV_dup634" "HERV_dup1099" "HERV_dup1327" "HERV_dup133" "HERV_dup509"
## [676] "HERV_dup1459" "HERV_dup2942" "HERV_dup3181" "HERV_dup772" "HERV_dup177"
## [681] "HERV_dup1346" "HERV_dup2945" "HERV_dup183" "HERV_dup2356" "HERV_dup1146"
## [686] "HERV_dup1673" "HERV_dup2967" "HERV_dup981" "HERV_dup78" "HERV_dup3154"
## [691] "HERV_dup450" "HERV_dup1403" "HERV_dup1003" "HERV_dup381" "HERV_dup2972"
## [696] "HERV_dup2441" "HERV_dup1549" "HERV_dup2557" "HERV_dup930" "HERV_dup2894"
## [701] "HERV_dup846" "HERV_dup1322" "HERV_dup3219" "HERV_dup3137" "HERV_dup1943"
## [706] "HERV_dup1656" "HERV_dup1823" "HERV_dup2525" "HERV_dup452" "HERV_dup2464"
## [711] "HERV_dup1639" "HERV_dup1868" "HERV_dup447" "HERV_dup3588" "HERV_dup129"
## [716] "HERV_dup1752" "HERV_dup1514" "HERV_dup3606" "HERV_dup3016" "HERV_dup389"
## [721] "HERV_dup1239" "HERV_dup924" "HERV_dup1415" "HERV_dup2324" "HERV_dup398"
## [726] "HERV_dup1733" "HERV_dup2897" "HERV_dup850" "HERV_dup640" "HERV_dup2875"
## [731] "HERV_dup3189" "HERV_dup3545" "HERV_dup1958" "HERV_dup3015" "HERV_dup2479"
## [736] "HERV_dup400" "HERV_dup1172" "HERV_dup2743" "HERV_dup3607"
asap_heatmap_snRNA(region = c("SN"),
tes = data_TE_annotation[which(data_TE_annotation$type == "HERV"),"TE_id"],
return_df = F,
breaks = seq(0,15,length.out = 52),
data = TE_data,
group_cols = c("celltype"),
index_row_reorder = c(HERVs_sorted_sn),
order_cols_groups = order_cols_celltype,
title = "SN HERV: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
annotation_cols = annotation_cols)

## $heatmap
##
## $order_cols
## [1] "AA_ASAP129_ctrl_NP22-37_SN_1" "AA_ASAP118_PD_NP22-55_SN_1"
## [3] "DA792_ASAP51_ctrl_NP19-36_SN_1" "AA_ASAP137_PD_NP23-21_SN_1"
## [5] "DA487_ASAP8_ctrl_PT231_SN_1" "AA_ASAP133_PD_NP17-232_SN_2"
## [7] "AA_ASAP99_ctrl_NP16-284_SN_2" "DA784_ASAP46_ctrl_NP17-256_SN_2"
## [9] "DA431_ASAP4_PD_P74_SN_2" "DA479_ASAP7_ctrl_NP16-21_SN_2"
## [11] "AA_ASAP137_PD_NP23-21_SN_2" "DA794_ASAP54_ctrl_NP19-37_SN_2"
## [13] "AA_ASAP132_PD_NP16-285_SN_2" "DA433_ASAP5_ctrl_NP16-161_SN_2"
## [15] "DA475_ASAP2_PD_NP16-25_SN_2" "AA_ASAP129_ctrl_NP22-37_SN_2"
## [17] "AA_ASAP118_PD_NP22-55_SN_2" "DA782_ASAP41_PD_NP19-108_SN_2"
## [19] "AA_ASAP108_ctrl_NP18-148_SN_2" "MJ_ASAP6_ctrl_NP16-164_SN_2"
## [21] "DA487_ASAP8_ctrl_PT231_SN_2" "AA_ASAP104_ctrl_NP16-119_SN_2"
## [23] "DA429_ASAP1_PD_NP16-162_SN_2" "AA_ASAP135_PD_NP19-137_SN_2"
## [25] "AA_ASAP134_PD_NP19-91_SN_2" "DA473_ASAP38_PD_NP19-23_SN_2"
## [27] "AA_ASAP105_ctrl_NP16-293_SN_2" "DA796_ASAP57_ctrl_NP19-45_SN_2"
## [29] "AA_ASAP127_ctrl_NP19-218_SN_2" "DA792_ASAP51_ctrl_NP19-36_SN_2"
## [31] "AA_ASAP101_PD_NP21-57_SN_2" "AA_ASAP102_PD_NP21-208_SN_2"
## [33] "DA489_ASAP3_PD_P73_SN_2" "AA_ASAP103_PD_NP21-217_SN_2"
## [35] "DA511_ASAP21_PD_NP16-269_SN_2" "DA784_ASAP46_ctrl_NP17-256_SN_3"
## [37] "AA_ASAP99_ctrl_NP16-284_SN_3" "AA_ASAP134_PD_NP19-91_SN_3"
## [39] "DA433_ASAP5_ctrl_NP16-161_SN_3" "AA_ASAP129_ctrl_NP22-37_SN_3"
## [41] "DA431_ASAP4_PD_P74_SN_3" "AA_ASAP127_ctrl_NP19-218_SN_3"
## [43] "AA_ASAP136_PD_NP21-04_SN_3" "AA_ASAP133_PD_NP17-232_SN_3"
## [45] "AA_ASAP104_ctrl_NP16-119_SN_3" "DA796_ASAP57_ctrl_NP19-45_SN_3"
## [47] "DA479_ASAP7_ctrl_NP16-21_SN_3" "AA_ASAP101_PD_NP21-57_SN_3"
## [49] "DA489_ASAP3_PD_P73_SN_3" "DA792_ASAP51_ctrl_NP19-36_SN_3"
## [51] "DA475_ASAP2_PD_NP16-25_SN_3" "AA_ASAP137_PD_NP23-21_SN_3"
## [53] "AA_ASAP135_PD_NP19-137_SN_3" "DA511_ASAP21_PD_NP16-269_SN_3"
## [55] "DA782_ASAP41_PD_NP19-108_SN_3" "DA794_ASAP54_ctrl_NP19-37_SN_3"
## [57] "AA_ASAP102_PD_NP21-208_SN_3" "AA_ASAP103_PD_NP21-217_SN_3"
## [59] "AA_ASAP105_ctrl_NP16-293_SN_3" "DA473_ASAP38_PD_NP19-23_SN_3"
## [61] "AA_ASAP108_ctrl_NP18-148_SN_3" "MJ_ASAP6_ctrl_NP16-164_SN_3"
## [63] "AA_ASAP132_PD_NP16-285_SN_3" "DA429_ASAP1_PD_NP16-162_SN_3"
## [65] "AA_ASAP118_PD_NP22-55_SN_3" "DA487_ASAP8_ctrl_PT231_SN_3"
## [67] "AA_ASAP99_ctrl_NP16-284_SN_5" "AA_ASAP105_ctrl_NP16-293_SN_5"
## [69] "DA784_ASAP46_ctrl_NP17-256_SN_5" "AA_ASAP132_PD_NP16-285_SN_5"
## [71] "AA_ASAP102_PD_NP21-208_SN_5" "DA433_ASAP5_ctrl_NP16-161_SN_5"
## [73] "AA_ASAP108_ctrl_NP18-148_SN_5" "DA473_ASAP38_PD_NP19-23_SN_5"
## [75] "MJ_ASAP6_ctrl_NP16-164_SN_5" "AA_ASAP127_ctrl_NP19-218_SN_5"
## [77] "AA_ASAP129_ctrl_NP22-37_SN_5" "DA431_ASAP4_PD_P74_SN_5"
## [79] "AA_ASAP136_PD_NP21-04_SN_5" "AA_ASAP104_ctrl_NP16-119_SN_5"
## [81] "DA475_ASAP2_PD_NP16-25_SN_5" "DA489_ASAP3_PD_P73_SN_5"
## [83] "AA_ASAP101_PD_NP21-57_SN_5" "AA_ASAP103_PD_NP21-217_SN_5"
## [85] "DA511_ASAP21_PD_NP16-269_SN_5" "AA_ASAP135_PD_NP19-137_SN_5"
## [87] "DA792_ASAP51_ctrl_NP19-36_SN_5" "DA794_ASAP54_ctrl_NP19-37_SN_5"
## [89] "DA782_ASAP41_PD_NP19-108_SN_5" "AA_ASAP137_PD_NP23-21_SN_5"
## [91] "AA_ASAP118_PD_NP22-55_SN_5" "DA429_ASAP1_PD_NP16-162_SN_5"
## [93] "AA_ASAP134_PD_NP19-91_SN_5" "AA_ASAP133_PD_NP17-232_SN_5"
## [95] "DA479_ASAP7_ctrl_NP16-21_SN_5" "DA796_ASAP57_ctrl_NP19-45_SN_5"
## [97] "DA487_ASAP8_ctrl_PT231_SN_5" "AA_ASAP134_PD_NP19-91_SN_4"
## [99] "DA473_ASAP38_PD_NP19-23_SN_4" "AA_ASAP129_ctrl_NP22-37_SN_4"
## [101] "DA431_ASAP4_PD_P74_SN_4" "MJ_ASAP6_ctrl_NP16-164_SN_4"
## [103] "AA_ASAP118_PD_NP22-55_SN_4" "AA_ASAP108_ctrl_NP18-148_SN_4"
## [105] "DA433_ASAP5_ctrl_NP16-161_SN_4" "AA_ASAP102_PD_NP21-208_SN_4"
## [107] "DA489_ASAP3_PD_P73_SN_4" "DA511_ASAP21_PD_NP16-269_SN_4"
## [109] "AA_ASAP127_ctrl_NP19-218_SN_4" "AA_ASAP101_PD_NP21-57_SN_4"
## [111] "AA_ASAP103_PD_NP21-217_SN_4" "DA475_ASAP2_PD_NP16-25_SN_4"
## [113] "AA_ASAP104_ctrl_NP16-119_SN_4" "DA794_ASAP54_ctrl_NP19-37_SN_4"
## [115] "DA487_ASAP8_ctrl_PT231_SN_4" "DA782_ASAP41_PD_NP19-108_SN_4"
## [117] "AA_ASAP137_PD_NP23-21_SN_4" "DA429_ASAP1_PD_NP16-162_SN_4"
## [119] "AA_ASAP135_PD_NP19-137_SN_4" "DA792_ASAP51_ctrl_NP19-36_SN_4"
## [121] "AA_ASAP133_PD_NP17-232_SN_4" "DA792_ASAP51_ctrl_NP19-36_SN_6"
## [123] "AA_ASAP137_PD_NP23-21_SN_6" "AA_ASAP133_PD_NP17-232_SN_7"
## [125] "AA_ASAP108_ctrl_NP18-148_SN_7" "AA_ASAP137_PD_NP23-21_SN_7"
##
## $order_rows
## [1] "HERV_dup773" "HERV_dup1758" "HERV_dup1" "HERV_dup2491" "HERV_dup288"
## [6] "HERV_dup2856" "HERV_dup1281" "HERV_dup1209" "HERV_dup2966" "HERV_dup3390"
## [11] "HERV_dup1708" "HERV_dup926" "HERV_dup799" "HERV_dup1050" "HERV_dup302"
## [16] "HERV_dup940" "HERV_dup265" "HERV_dup600" "HERV_dup1702" "HERV_dup3252"
## [21] "HERV_dup2900" "HERV_dup2838" "HERV_dup2880" "HERV_dup3357" "HERV_dup1079"
## [26] "HERV_dup2841" "HERV_dup2603" "HERV_dup2273" "HERV_dup1339" "HERV_dup152"
## [31] "HERV_dup54" "HERV_dup1283" "HERV_dup1000" "HERV_dup1356" "HERV_dup470"
## [36] "HERV_dup2789" "HERV_dup3105" "HERV_dup1357" "HERV_dup1888" "HERV_dup379"
## [41] "HERV_dup1669" "HERV_dup1036" "HERV_dup93" "HERV_dup1456" "HERV_dup1002"
## [46] "HERV_dup980" "HERV_dup614" "HERV_dup2376" "HERV_dup1359" "HERV_dup1598"
## [51] "HERV_dup562" "HERV_dup2381" "HERV_dup2879" "HERV_dup1004" "HERV_dup3379"
## [56] "HERV_dup2365" "HERV_dup1657" "HERV_dup1102" "HERV_dup717" "HERV_dup3226"
## [61] "HERV_dup112" "HERV_dup2182" "HERV_dup2292" "HERV_dup2902" "HERV_dup209"
## [66] "HERV_dup2299" "HERV_dup474" "HERV_dup3423" "HERV_dup34" "HERV_dup1308"
## [71] "HERV_dup966" "HERV_dup3266" "HERV_dup417" "HERV_dup1052" "HERV_dup1701"
## [76] "HERV_dup1203" "HERV_dup3171" "HERV_dup3174" "HERV_dup3375" "HERV_dup1309"
## [81] "HERV_dup1334" "HERV_dup1310" "HERV_dup3343" "HERV_dup2217" "HERV_dup731"
## [86] "HERV_dup1934" "HERV_dup873" "HERV_dup1667" "HERV_dup2530" "HERV_dup2012"
## [91] "HERV_dup612" "HERV_dup1255" "HERV_dup1007" "HERV_dup1319" "HERV_dup3363"
## [96] "HERV_dup1362" "HERV_dup3522" "HERV_dup904" "HERV_dup384" "HERV_dup597"
## [101] "HERV_dup1382" "HERV_dup1875" "HERV_dup3013" "HERV_dup758" "HERV_dup1345"
## [106] "HERV_dup3418" "HERV_dup301" "HERV_dup1670" "HERV_dup3694" "HERV_dup518"
## [111] "HERV_dup1755" "HERV_dup880" "HERV_dup2840" "HERV_dup2589" "HERV_dup110"
## [116] "HERV_dup2438" "HERV_dup2643" "HERV_dup2914" "HERV_dup151" "HERV_dup1282"
## [121] "HERV_dup37" "HERV_dup899" "HERV_dup1663" "HERV_dup3107" "HERV_dup1611"
## [126] "HERV_dup1447" "HERV_dup916" "HERV_dup2752" "HERV_dup203" "HERV_dup1001"
## [131] "HERV_dup2843" "HERV_dup2261" "HERV_dup2192" "HERV_dup2847" "HERV_dup1449"
## [136] "HERV_dup3355" "HERV_dup2631" "HERV_dup118" "HERV_dup3020" "HERV_dup1048"
## [141] "HERV_dup57" "HERV_dup1315" "HERV_dup1017" "HERV_dup292" "HERV_dup1846"
## [146] "HERV_dup1358" "HERV_dup1940" "HERV_dup2106" "HERV_dup1776" "HERV_dup1253"
## [151] "HERV_dup1694" "HERV_dup2891" "HERV_dup2111" "HERV_dup3050" "HERV_dup18"
## [156] "HERV_dup2550" "HERV_dup2415" "HERV_dup3231" "HERV_dup1351" "HERV_dup1512"
## [161] "HERV_dup1750" "HERV_dup954" "HERV_dup5" "HERV_dup1302" "HERV_dup967"
## [166] "HERV_dup2481" "HERV_dup2320" "HERV_dup2588" "HERV_dup1107" "HERV_dup979"
## [171] "HERV_dup2784" "HERV_dup1240" "HERV_dup1374" "HERV_dup1242" "HERV_dup661"
## [176] "HERV_dup573" "HERV_dup380" "HERV_dup670" "HERV_dup1662" "HERV_dup2961"
## [181] "HERV_dup482" "HERV_dup1596" "HERV_dup356" "HERV_dup599" "HERV_dup467"
## [186] "HERV_dup3198" "HERV_dup2129" "HERV_dup1243" "HERV_dup2176" "HERV_dup3417"
## [191] "HERV_dup355" "HERV_dup831" "HERV_dup1232" "HERV_dup65" "HERV_dup2936"
## [196] "HERV_dup2834" "HERV_dup290" "HERV_dup872" "HERV_dup1720" "HERV_dup1269"
## [201] "HERV_dup1071" "HERV_dup3529" "HERV_dup682" "HERV_dup1081" "HERV_dup956"
## [206] "HERV_dup509" "HERV_dup3220" "HERV_dup2235" "HERV_dup1802" "HERV_dup2476"
## [211] "HERV_dup3015" "HERV_dup968" "HERV_dup2266" "HERV_dup2166" "HERV_dup2877"
## [216] "HERV_dup2179" "HERV_dup1371" "HERV_dup1847" "HERV_dup2041" "HERV_dup913"
## [221] "HERV_dup3430" "HERV_dup433" "HERV_dup1569" "HERV_dup1208" "HERV_dup662"
## [226] "HERV_dup487" "HERV_dup1187" "HERV_dup1236" "HERV_dup2242" "HERV_dup1484"
## [231] "HERV_dup2183" "HERV_dup471" "HERV_dup26" "HERV_dup2733" "HERV_dup94"
## [236] "HERV_dup3580" "HERV_dup3239" "HERV_dup2412" "HERV_dup1073" "HERV_dup1112"
## [241] "HERV_dup3140" "HERV_dup3187" "HERV_dup1935" "HERV_dup2298" "HERV_dup2163"
## [246] "HERV_dup282" "HERV_dup939" "HERV_dup419" "HERV_dup409" "HERV_dup890"
## [251] "HERV_dup2662" "HERV_dup732" "HERV_dup2566" "HERV_dup2939" "HERV_dup2391"
## [256] "HERV_dup1917" "HERV_dup1931" "HERV_dup2735" "HERV_dup2857" "HERV_dup2719"
## [261] "HERV_dup1272" "HERV_dup108" "HERV_dup180" "HERV_dup2188" "HERV_dup1316"
## [266] "HERV_dup1756" "HERV_dup1331" "HERV_dup249" "HERV_dup1780" "HERV_dup2769"
## [271] "HERV_dup1613" "HERV_dup990" "HERV_dup293" "HERV_dup2623" "HERV_dup1459"
## [276] "HERV_dup2812" "HERV_dup3388" "HERV_dup443" "HERV_dup949" "HERV_dup2941"
## [281] "HERV_dup1235" "HERV_dup272" "HERV_dup2085" "HERV_dup1717" "HERV_dup2801"
## [286] "HERV_dup2803" "HERV_dup1213" "HERV_dup173" "HERV_dup3341" "HERV_dup3519"
## [291] "HERV_dup1661" "HERV_dup1749" "HERV_dup3410" "HERV_dup1303" "HERV_dup1090"
## [296] "HERV_dup1731" "HERV_dup468" "HERV_dup3408" "HERV_dup3406" "HERV_dup1324"
## [301] "HERV_dup2964" "HERV_dup556" "HERV_dup202" "HERV_dup2599" "HERV_dup2379"
## [306] "HERV_dup1089" "HERV_dup1703" "HERV_dup1438" "HERV_dup1297" "HERV_dup3016"
## [311] "HERV_dup2500" "HERV_dup3124" "HERV_dup2383" "HERV_dup626" "HERV_dup2604"
## [316] "HERV_dup3033" "HERV_dup2598" "HERV_dup876" "HERV_dup1513" "HERV_dup1889"
## [321] "HERV_dup2963" "HERV_dup3251" "HERV_dup1932" "HERV_dup2366" "HERV_dup1605"
## [326] "HERV_dup1046" "HERV_dup389" "HERV_dup1719" "HERV_dup2915" "HERV_dup1114"
## [331] "HERV_dup2653" "HERV_dup2736" "HERV_dup3270" "HERV_dup554" "HERV_dup2158"
## [336] "HERV_dup2533" "HERV_dup2264" "HERV_dup2525" "HERV_dup377" "HERV_dup2962"
## [341] "HERV_dup1526" "HERV_dup3063" "HERV_dup348" "HERV_dup1671" "HERV_dup214"
## [346] "HERV_dup3148" "HERV_dup1587" "HERV_dup3342" "HERV_dup2353" "HERV_dup1416"
## [351] "HERV_dup36" "HERV_dup2033" "HERV_dup2949" "HERV_dup2728" "HERV_dup1920"
## [356] "HERV_dup1222" "HERV_dup2934" "HERV_dup1496" "HERV_dup183" "HERV_dup2548"
## [361] "HERV_dup1891" "HERV_dup1617" "HERV_dup1707" "HERV_dup692" "HERV_dup331"
## [366] "HERV_dup2250" "HERV_dup3358" "HERV_dup2422" "HERV_dup1245" "HERV_dup613"
## [371] "HERV_dup1653" "HERV_dup1321" "HERV_dup2480" "HERV_dup300" "HERV_dup344"
## [376] "HERV_dup1248" "HERV_dup2905" "HERV_dup729" "HERV_dup3227" "HERV_dup2878"
## [381] "HERV_dup640" "HERV_dup2019" "HERV_dup1298" "HERV_dup2027" "HERV_dup58"
## [386] "HERV_dup710" "HERV_dup218" "HERV_dup1730" "HERV_dup3351" "HERV_dup632"
## [391] "HERV_dup1317" "HERV_dup3287" "HERV_dup1268" "HERV_dup2112" "HERV_dup2632"
## [396] "HERV_dup909" "HERV_dup3505" "HERV_dup1029" "HERV_dup1156" "HERV_dup2607"
## [401] "HERV_dup772" "HERV_dup61" "HERV_dup928" "HERV_dup2334" "HERV_dup517"
## [406] "HERV_dup84" "HERV_dup329" "HERV_dup933" "HERV_dup3365" "HERV_dup1972"
## [411] "HERV_dup1201" "HERV_dup1982" "HERV_dup1064" "HERV_dup2907" "HERV_dup3416"
## [416] "HERV_dup1307" "HERV_dup386" "HERV_dup3507" "HERV_dup1322" "HERV_dup27"
## [421] "HERV_dup1973" "HERV_dup2436" "HERV_dup2303" "HERV_dup1210" "HERV_dup631"
## [426] "HERV_dup2848" "HERV_dup1733" "HERV_dup1953" "HERV_dup3100" "HERV_dup882"
## [431] "HERV_dup927" "HERV_dup441" "HERV_dup852" "HERV_dup2739" "HERV_dup1239"
## [436] "HERV_dup194" "HERV_dup388" "HERV_dup1129" "HERV_dup120" "HERV_dup776"
## [441] "HERV_dup3118" "HERV_dup565" "HERV_dup553" "HERV_dup1279" "HERV_dup1614"
## [446] "HERV_dup1658" "HERV_dup969" "HERV_dup1494" "HERV_dup519" "HERV_dup1869"
## [451] "HERV_dup2561" "HERV_dup724" "HERV_dup1872" "HERV_dup2804" "HERV_dup243"
## [456] "HERV_dup1579" "HERV_dup2128" "HERV_dup29" "HERV_dup746" "HERV_dup2141"
## [461] "HERV_dup736" "HERV_dup2134" "HERV_dup2555" "HERV_dup2747" "HERV_dup1003"
## [466] "HERV_dup276" "HERV_dup38" "HERV_dup2778" "HERV_dup381" "HERV_dup1366"
## [471] "HERV_dup586" "HERV_dup1394" "HERV_dup1131" "HERV_dup314" "HERV_dup1890"
## [476] "HERV_dup21" "HERV_dup447" "HERV_dup3394" "HERV_dup1295" "HERV_dup2886"
## [481] "HERV_dup2002" "HERV_dup803" "HERV_dup1005" "HERV_dup2324" "HERV_dup634"
## [486] "HERV_dup488" "HERV_dup321" "HERV_dup115" "HERV_dup1285" "HERV_dup934"
## [491] "HERV_dup2646" "HERV_dup2602" "HERV_dup777" "HERV_dup1333" "HERV_dup665"
## [496] "HERV_dup2855" "HERV_dup2635" "HERV_dup291" "HERV_dup215" "HERV_dup1541"
## [501] "HERV_dup703" "HERV_dup434" "HERV_dup1014" "HERV_dup1778" "HERV_dup884"
## [506] "HERV_dup1914" "HERV_dup1500" "HERV_dup1948" "HERV_dup975" "HERV_dup1433"
## [511] "HERV_dup2093" "HERV_dup1384" "HERV_dup1184" "HERV_dup1668" "HERV_dup2772"
## [516] "HERV_dup1724" "HERV_dup3182" "HERV_dup894" "HERV_dup1390" "HERV_dup870"
## [521] "HERV_dup2187" "HERV_dup127" "HERV_dup3143" "HERV_dup2985" "HERV_dup2743"
## [526] "HERV_dup1047" "HERV_dup1417" "HERV_dup469" "HERV_dup2937" "HERV_dup2152"
## [531] "HERV_dup1413" "HERV_dup578" "HERV_dup129" "HERV_dup851" "HERV_dup2557"
## [536] "HERV_dup3181" "HERV_dup369" "HERV_dup251" "HERV_dup3286" "HERV_dup407"
## [541] "HERV_dup1851" "HERV_dup2319" "HERV_dup2663" "HERV_dup2518" "HERV_dup1038"
## [546] "HERV_dup2282" "HERV_dup551" "HERV_dup2655" "HERV_dup1412" "HERV_dup1437"
## [551] "HERV_dup1304" "HERV_dup3008" "HERV_dup850" "HERV_dup728" "HERV_dup1212"
## [556] "HERV_dup1403" "HERV_dup981" "HERV_dup2536" "HERV_dup184" "HERV_dup1453"
## [561] "HERV_dup1093" "HERV_dup1937" "HERV_dup2894" "HERV_dup250" "HERV_dup2875"
## [566] "HERV_dup723" "HERV_dup1108" "HERV_dup1923" "HERV_dup3073" "HERV_dup1082"
## [571] "HERV_dup446" "HERV_dup1555" "HERV_dup185" "HERV_dup1389" "HERV_dup3137"
## [576] "HERV_dup1958" "HERV_dup3108" "HERV_dup1378" "HERV_dup1350" "HERV_dup1491"
## [581] "HERV_dup2100" "HERV_dup2278" "HERV_dup570" "HERV_dup1470" "HERV_dup3366"
## [586] "HERV_dup2651" "HERV_dup508" "HERV_dup2524" "HERV_dup1629" "HERV_dup461"
## [591] "HERV_dup577" "HERV_dup1278" "HERV_dup1655" "HERV_dup505" "HERV_dup2647"
## [596] "HERV_dup2562" "HERV_dup2441" "HERV_dup1381" "HERV_dup1514" "HERV_dup3189"
## [601] "HERV_dup1804" "HERV_dup23" "HERV_dup3210" "HERV_dup2972" "HERV_dup2034"
## [606] "HERV_dup1273" "HERV_dup2130" "HERV_dup2967" "HERV_dup3481" "HERV_dup2896"
## [611] "HERV_dup1902" "HERV_dup572" "HERV_dup1926" "HERV_dup3031" "HERV_dup3606"
## [616] "HERV_dup3117" "HERV_dup568" "HERV_dup2809" "HERV_dup900" "HERV_dup977"
## [621] "HERV_dup1527" "HERV_dup2706" "HERV_dup1638" "HERV_dup1979" "HERV_dup924"
## [626] "HERV_dup3212" "HERV_dup2482" "HERV_dup2404" "HERV_dup846" "HERV_dup492"
## [631] "HERV_dup1080" "HERV_dup1401" "HERV_dup86" "HERV_dup39" "HERV_dup3154"
## [636] "HERV_dup1823" "HERV_dup1228" "HERV_dup1556" "HERV_dup177" "HERV_dup1195"
## [641] "HERV_dup2696" "HERV_dup78" "HERV_dup2378" "HERV_dup2272" "HERV_dup3248"
## [646] "HERV_dup3215" "HERV_dup2945" "HERV_dup1327" "HERV_dup2977" "HERV_dup1103"
## [651] "HERV_dup2695" "HERV_dup3179" "HERV_dup399" "HERV_dup1146" "HERV_dup1557"
## [656] "HERV_dup3319" "HERV_dup17" "HERV_dup2149" "HERV_dup2479" "HERV_dup2464"
## [661] "HERV_dup1049" "HERV_dup3217" "HERV_dup1933" "HERV_dup133" "HERV_dup1640"
## [666] "HERV_dup3588" "HERV_dup530" "HERV_dup2942" "HERV_dup3131" "HERV_dup1254"
## [671] "HERV_dup595" "HERV_dup3673" "HERV_dup1664" "HERV_dup1757" "HERV_dup2337"
## [676] "HERV_dup2620" "HERV_dup1962" "HERV_dup1673" "HERV_dup1868" "HERV_dup1639"
## [681] "HERV_dup277" "HERV_dup982" "HERV_dup3219" "HERV_dup201" "HERV_dup3044"
## [686] "HERV_dup1943" "HERV_dup1013" "HERV_dup350" "HERV_dup357" "HERV_dup1218"
## [691] "HERV_dup2823" "HERV_dup2356" "HERV_dup3037" "HERV_dup2137" "HERV_dup1440"
## [696] "HERV_dup1346" "HERV_dup1944" "HERV_dup1182" "HERV_dup3328" "HERV_dup2978"
## [701] "HERV_dup3459" "HERV_dup1383" "HERV_dup1656" "HERV_dup739" "HERV_dup1172"
## [706] "HERV_dup671" "HERV_dup1532" "HERV_dup3196" "HERV_dup2730" "HERV_dup935"
## [711] "HERV_dup2897" "HERV_dup2797" "HERV_dup1415" "HERV_dup1752" "HERV_dup2290"
## [716] "HERV_dup240" "HERV_dup2159" "HERV_dup1520" "HERV_dup2680" "HERV_dup1364"
## [721] "HERV_dup2979" "HERV_dup930" "HERV_dup2785" "HERV_dup591" "HERV_dup2529"
## [726] "HERV_dup3607" "HERV_dup735" "HERV_dup1099" "HERV_dup1549" "HERV_dup1711"
## [731] "HERV_dup3284" "HERV_dup3335" "HERV_dup336" "HERV_dup3545" "HERV_dup3688"
## [736] "HERV_dup398" "HERV_dup400" "HERV_dup450" "HERV_dup452"
8.2 Pseudobulk heatmaps clustering rows
- Heatmap visualization of expressed >6kbp L1HS-L1PA3 and HERVs on
pseudobulks with more than 50 nuclei (line 318).
- Rows are clustered using a hierarchical clustering method within
pheatmap.
- Excluded clusters 6 (VLMC) and 7 (Tcells) due to low number of
nuclei.
I wanted to have the heatmaps of L1s and HERVs stacked but
not mixed, so I’m collecting the order of the row clustering in a
variable of shape heatmap_[region]_[TE]_order.
heatmap_pfc_L1 <- asap_heatmap_snRNA(region = c("PFC"),
tes = data_TE_annotation[which(data_TE_annotation$type == "L1"),"TE_id"],
return_df = F,
breaks = seq(0,15,length.out = 52),
group_rows = c("type"),
data = TE_data, group_cols = c("celltype"),
order_cols_groups = order_cols_celltype,
title = "PFC L1s: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
exclude_clusters = c(6, 7))

heatmap_pfc_L1_order <- heatmap_pfc_L1$order_rows
heatmap_pfc_HERV <- asap_heatmap_snRNA(region = c("PFC"),
tes = data_TE_annotation[which(data_TE_annotation$type == "HERV"),"TE_id"],
return_df = F,
group_rows = c("type"),
breaks = seq(0,15,length.out = 52),
data = TE_data, group_cols = c("celltype"),
order_cols_groups = order_cols_celltype,
title = "PFC HERVs: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
exclude_clusters = c(6, 7))

heatmap_pfc_HERV_order <- heatmap_pfc_HERV$order_rows
heatmap_put_L1 <- asap_heatmap_snRNA(region = c("PUT"),
tes = data_TE_annotation[which(data_TE_annotation$type == "L1"),"TE_id"],
return_df = F,
group_rows = c("type"),
breaks = seq(0,15,length.out = 52),
data = TE_data, group_cols = c("celltype"),
order_cols_groups = order_cols_celltype,
title = "PUT L1s: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
exclude_clusters = c(6, 7))

heatmap_put_L1_order <- heatmap_put_L1$order_rows
heatmap_put_HERV <- asap_heatmap_snRNA(region = c("PUT"),
tes = data_TE_annotation[which(data_TE_annotation$type == "HERV"),"TE_id"],
return_df = F,
group_rows = c("type"),
breaks = seq(0,15,length.out = 52),
data = TE_data, group_cols = c("celltype"),
order_cols_groups = order_cols_celltype,
title = "PUT HERVs: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
exclude_clusters = c(6, 7))

heatmap_put_HERV_order <- heatmap_put_HERV$order_rows
heatmap_sn_L1 <- asap_heatmap_snRNA(region = c("SN"),
tes = data_TE_annotation[which(data_TE_annotation$type == "L1"),"TE_id"],
return_df = F,
group_rows = c("type"),
breaks = seq(0,15,length.out = 52),
data = TE_data, group_cols = c("celltype"),
order_cols_groups = order_cols_celltype,
title = "SN L1s: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
exclude_clusters = c(6, 7))

heatmap_sn_L1_order <- heatmap_sn_L1$order_rows
heatmap_sn_HERV <- asap_heatmap_snRNA(region = c("SN"),
tes = data_TE_annotation[which(data_TE_annotation$type == "HERV"),"TE_id"],
return_df = F,
group_rows = c("type"),
breaks = seq(0,15,length.out = 52),
data = TE_data, group_cols = c("celltype"),
order_cols_groups = order_cols_celltype,
title = "SN HERVs: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
exclude_clusters = c(6, 7))

heatmap_sn_HERV_order <- heatmap_sn_HERV$order_rows
heatmap_amy_L1 <- asap_heatmap_snRNA(region = c("AMY"),
tes = data_TE_annotation[which(data_TE_annotation$type == "L1"),"TE_id"],
return_df = F,
group_rows = c("type"),
breaks = seq(0,15,length.out = 52),
data = TE_data, group_cols = c("celltype"),
order_cols_groups = order_cols_celltype,
title = "AMY L1s: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
exclude_clusters = c(6, 7))

heatmap_amy_L1_order <- heatmap_amy_L1$order_rows
heatmap_amy_HERV <- asap_heatmap_snRNA(region = c("AMY"),
tes = data_TE_annotation[which(data_TE_annotation$type == "HERV"),"TE_id"],
return_df = F,
group_rows = c("type"),
breaks = seq(0,15,length.out = 52),
data = TE_data, group_cols = c("celltype"),
order_cols_groups = order_cols_celltype,
title = "AMY HERVs: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
exclude_clusters = c(6, 7))

heatmap_amy_HERV_order <- heatmap_amy_HERV$order_rows
Figure stacked heatmaps
I’m using the variables heatmap_[region]_[TE]_order to
stack the L1 and HERV heatmaps on top of each other. These are the
heatmaps shown in figure 3.
asap_heatmap_snRNA(region = c("PFC"),
tes = data_TE_annotation$TE_id,
return_df = F, group_rows = c("type"),
gaps_row = length(heatmap_pfc_HERV_order),
breaks = seq(0,15,length.out = 52), index_row_reorder = c(heatmap_pfc_HERV_order,heatmap_pfc_L1_order),
order_cols_groups = order_cols_celltype,
data = TE_data, group_cols = c("celltype"),
title = "PFC HERVs + L1s: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
exclude_clusters = c(6, 7))

## $heatmap
##
## $order_cols
## [1] "DA813_ASAP17_PD_NP16-140_PFC_0" "DA804_ASAP49_ctrl_NP18-159_PFC_0"
## [3] "DA775_ASAP22_PD_NP16-269_PFC_0" "AA_ASAP81_PD_NP21-208_PFC_0"
## [5] "AA_ASAP91_ctrl_NP17-20_PFC_0" "AA_ASAP85_NP18-46_ctrl_PFC_0"
## [7] "MJ_ASAP14_ctrl_NP16-164_PFC_0" "AA_ASAP151_PD_NP17-232_PFC_0"
## [9] "ASAP155_ctrl_NP23-21_PFC_0" "AA_ASAP116_PD_NP22-55_PFC_0"
## [11] "AA_ASAP152_PD_NP19-91_PFC_0" "AA_ASAP89_ctrl_NP16-284_PFC_0"
## [13] "AA_ASAP90_ctrl_NP16-293_PFC_0" "AA_ASAP145_ctrl_NP19-218_PFC_0"
## [15] "DA480_ASAP15_ctrl_NP16-21_PFC_0" "DA795_ASAP55_ctrl_NP19-37_PFC_0"
## [17] "DA476_ASAP10_PD_NP16-25_PFC_0" "AA_ASAP82_PD_NP21-217_PFC_0"
## [19] "DA809_ASAP30_PD_NP18-117_PFC_0" "DA777_ASAP28_PD_NP17-191_PFC_0"
## [21] "DA499_ASAP44_PD_NP19-255_PFC_0" "AA_ASAP153_ctrl_NP19-137_PFC_0"
## [23] "DA432_ASAP12_PD_P74_PFC_0" "DA806_ASAP58_ctrl_NP19-45_PFC_0"
## [25] "DA488_ASAP16_ctrl_PT231_PFC_0" "DA428_ASAP13_ctrl_NP16-161_PFC_0"
## [27] "DA810_ASAP34_PD_NP18-304_PFC_0" "AA_ASAP83_NP16-119_ctrl_PFC_0"
## [29] "DA430_ASAP9_PD_NP16-162_PFC_0" "DA509_ASAP36_PD_NP19-16_PFC_0"
## [31] "DA490_ASAP11_PD_P73_PFC_0" "AA_ASAP80_PD_NP21-57_PFC_0"
## [33] "AA_ASAP86_NP18-148_ctrl_PFC_0" "AA_ASAP90_ctrl_NP16-293_PFC_1"
## [35] "AA_ASAP89_ctrl_NP16-284_PFC_1" "DA490_ASAP11_PD_P73_PFC_1"
## [37] "DA509_ASAP36_PD_NP19-16_PFC_1" "ASAP155_ctrl_NP23-21_PFC_1"
## [39] "AA_ASAP116_PD_NP22-55_PFC_1" "MJ_ASAP14_ctrl_NP16-164_PFC_1"
## [41] "AA_ASAP151_PD_NP17-232_PFC_1" "DA795_ASAP55_ctrl_NP19-37_PFC_1"
## [43] "AA_ASAP153_ctrl_NP19-137_PFC_1" "AA_ASAP91_ctrl_NP17-20_PFC_1"
## [45] "AA_ASAP85_NP18-46_ctrl_PFC_1" "DA480_ASAP15_ctrl_NP16-21_PFC_1"
## [47] "AA_ASAP145_ctrl_NP19-218_PFC_1" "AA_ASAP82_PD_NP21-217_PFC_1"
## [49] "AA_ASAP81_PD_NP21-208_PFC_1" "DA777_ASAP28_PD_NP17-191_PFC_1"
## [51] "DA809_ASAP30_PD_NP18-117_PFC_1" "AA_ASAP86_NP18-148_ctrl_PFC_1"
## [53] "AA_ASAP83_NP16-119_ctrl_PFC_1" "DA430_ASAP9_PD_NP16-162_PFC_1"
## [55] "DA476_ASAP10_PD_NP16-25_PFC_1" "DA488_ASAP16_ctrl_PT231_PFC_1"
## [57] "DA810_ASAP34_PD_NP18-304_PFC_1" "DA806_ASAP58_ctrl_NP19-45_PFC_1"
## [59] "DA428_ASAP13_ctrl_NP16-161_PFC_1" "AA_ASAP152_PD_NP19-91_PFC_1"
## [61] "DA432_ASAP12_PD_P74_PFC_1" "DA499_ASAP44_PD_NP19-255_PFC_1"
## [63] "AA_ASAP80_PD_NP21-57_PFC_1" "DA804_ASAP49_ctrl_NP18-159_PFC_1"
## [65] "DA775_ASAP22_PD_NP16-269_PFC_1" "AA_ASAP150_PD_NP16-285_PFC_2"
## [67] "DA785_ASAP47_ctrl_NP17-256_PFC_2" "AA_ASAP81_PD_NP21-208_PFC_2"
## [69] "DA490_ASAP11_PD_P73_PFC_2" "DA509_ASAP36_PD_NP19-16_PFC_2"
## [71] "DA432_ASAP12_PD_P74_PFC_2" "AA_ASAP84_NP17-216_ctrl_PFC_2"
## [73] "AA_ASAP154_ctrl_NP21-04_PFC_2" "AA_ASAP91_ctrl_NP17-20_PFC_2"
## [75] "AA_ASAP145_ctrl_NP19-218_PFC_2" "DA795_ASAP55_ctrl_NP19-37_PFC_2"
## [77] "DA476_ASAP10_PD_NP16-25_PFC_2" "AA_ASAP151_PD_NP17-232_PFC_2"
## [79] "DA430_ASAP9_PD_NP16-162_PFC_2" "AA_ASAP83_NP16-119_ctrl_PFC_2"
## [81] "AA_ASAP80_PD_NP21-57_PFC_2" "DA806_ASAP58_ctrl_NP19-45_PFC_2"
## [83] "DA810_ASAP34_PD_NP18-304_PFC_2" "AA_ASAP116_PD_NP22-55_PFC_2"
## [85] "AA_ASAP89_ctrl_NP16-284_PFC_2" "AA_ASAP86_NP18-148_ctrl_PFC_2"
## [87] "DA480_ASAP15_ctrl_NP16-21_PFC_2" "MJ_ASAP14_ctrl_NP16-164_PFC_2"
## [89] "DA499_ASAP44_PD_NP19-255_PFC_2" "DA428_ASAP13_ctrl_NP16-161_PFC_2"
## [91] "AA_ASAP152_PD_NP19-91_PFC_2" "DA488_ASAP16_ctrl_PT231_PFC_2"
## [93] "AA_ASAP90_ctrl_NP16-293_PFC_2" "AA_ASAP82_PD_NP21-217_PFC_2"
## [95] "AA_ASAP153_ctrl_NP19-137_PFC_2" "ASAP155_ctrl_NP23-21_PFC_2"
## [97] "DA808_ASAP41_PD_NP19-108_PFC_2" "DA775_ASAP22_PD_NP16-269_PFC_2"
## [99] "DA809_ASAP30_PD_NP18-117_PFC_2" "DA804_ASAP49_ctrl_NP18-159_PFC_2"
## [101] "AA_ASAP84_NP17-216_ctrl_PFC_3" "AA_ASAP154_ctrl_NP21-04_PFC_3"
## [103] "AA_ASAP91_ctrl_NP17-20_PFC_3" "AA_ASAP150_PD_NP16-285_PFC_3"
## [105] "AA_ASAP145_ctrl_NP19-218_PFC_3" "DA432_ASAP12_PD_P74_PFC_3"
## [107] "ASAP155_ctrl_NP23-21_PFC_3" "AA_ASAP86_NP18-148_ctrl_PFC_3"
## [109] "AA_ASAP152_PD_NP19-91_PFC_3" "DA509_ASAP36_PD_NP19-16_PFC_3"
## [111] "AA_ASAP90_ctrl_NP16-293_PFC_3" "DA490_ASAP11_PD_P73_PFC_3"
## [113] "DA775_ASAP22_PD_NP16-269_PFC_3" "DA795_ASAP55_ctrl_NP19-37_PFC_3"
## [115] "DA476_ASAP10_PD_NP16-25_PFC_3" "DA804_ASAP49_ctrl_NP18-159_PFC_3"
## [117] "DA809_ASAP30_PD_NP18-117_PFC_3" "DA430_ASAP9_PD_NP16-162_PFC_3"
## [119] "DA810_ASAP34_PD_NP18-304_PFC_3" "DA428_ASAP13_ctrl_NP16-161_PFC_3"
## [121] "DA488_ASAP16_ctrl_PT231_PFC_3" "AA_ASAP80_PD_NP21-57_PFC_3"
## [123] "DA806_ASAP58_ctrl_NP19-45_PFC_3" "DA499_ASAP44_PD_NP19-255_PFC_3"
## [125] "AA_ASAP83_NP16-119_ctrl_PFC_3" "AA_ASAP82_PD_NP21-217_PFC_3"
## [127] "DA480_ASAP15_ctrl_NP16-21_PFC_3" "DA777_ASAP28_PD_NP17-191_PFC_3"
## [129] "AA_ASAP89_ctrl_NP16-284_PFC_3" "AA_ASAP151_PD_NP17-232_PFC_3"
## [131] "AA_ASAP116_PD_NP22-55_PFC_3" "MJ_ASAP14_ctrl_NP16-164_PFC_3"
## [133] "DA785_ASAP47_ctrl_NP17-256_PFC_3" "DA785_ASAP47_ctrl_NP17-256_PFC_5"
## [135] "MJ_ASAP14_ctrl_NP16-164_PFC_5" "ASAP155_ctrl_NP23-21_PFC_5"
## [137] "AA_ASAP153_ctrl_NP19-137_PFC_5" "AA_ASAP85_NP18-46_ctrl_PFC_5"
## [139] "AA_ASAP91_ctrl_NP17-20_PFC_5" "AA_ASAP83_NP16-119_ctrl_PFC_5"
## [141] "DA428_ASAP13_ctrl_NP16-161_PFC_5" "AA_ASAP90_ctrl_NP16-293_PFC_5"
## [143] "DA430_ASAP9_PD_NP16-162_PFC_5" "AA_ASAP89_ctrl_NP16-284_PFC_5"
## [145] "DA432_ASAP12_PD_P74_PFC_5" "DA490_ASAP11_PD_P73_PFC_5"
## [147] "DA509_ASAP36_PD_NP19-16_PFC_5" "AA_ASAP84_NP17-216_ctrl_PFC_5"
## [149] "AA_ASAP154_ctrl_NP21-04_PFC_5" "DA799_ASAP19_PD_NP16-160_PFC_5"
## [151] "DA813_ASAP17_PD_NP16-140_PFC_5" "DA808_ASAP41_PD_NP19-108_PFC_5"
## [153] "AA_ASAP150_PD_NP16-285_PFC_5" "AA_ASAP151_PD_NP17-232_PFC_5"
## [155] "DA809_ASAP30_PD_NP18-117_PFC_5" "DA804_ASAP49_ctrl_NP18-159_PFC_5"
## [157] "DA476_ASAP10_PD_NP16-25_PFC_5" "DA795_ASAP55_ctrl_NP19-37_PFC_5"
## [159] "AA_ASAP116_PD_NP22-55_PFC_5" "AA_ASAP147_ctrl_NP22-37_PFC_5"
## [161] "DA775_ASAP22_PD_NP16-269_PFC_5" "DA480_ASAP15_ctrl_NP16-21_PFC_5"
## [163] "DA777_ASAP28_PD_NP17-191_PFC_5" "DA806_ASAP58_ctrl_NP19-45_PFC_5"
## [165] "AA_ASAP152_PD_NP19-91_PFC_5" "AA_ASAP145_ctrl_NP19-218_PFC_5"
## [167] "AA_ASAP86_NP18-148_ctrl_PFC_5" "DA499_ASAP44_PD_NP19-255_PFC_5"
## [169] "AA_ASAP82_PD_NP21-217_PFC_5" "AA_ASAP80_PD_NP21-57_PFC_5"
## [171] "DA488_ASAP16_ctrl_PT231_PFC_5" "DA810_ASAP34_PD_NP18-304_PFC_5"
## [173] "DA775_ASAP22_PD_NP16-269_PFC_4" "AA_ASAP89_ctrl_NP16-284_PFC_4"
## [175] "AA_ASAP90_ctrl_NP16-293_PFC_4" "DA428_ASAP13_ctrl_NP16-161_PFC_4"
## [177] "DA488_ASAP16_ctrl_PT231_PFC_4" "AA_ASAP80_PD_NP21-57_PFC_4"
## [179] "AA_ASAP152_PD_NP19-91_PFC_4" "AA_ASAP82_PD_NP21-217_PFC_4"
## [181] "AA_ASAP151_PD_NP17-232_PFC_4" "AA_ASAP83_NP16-119_ctrl_PFC_4"
## [183] "DA806_ASAP58_ctrl_NP19-45_PFC_4" "AA_ASAP145_ctrl_NP19-218_PFC_4"
## [185] "AA_ASAP86_NP18-148_ctrl_PFC_4" "DA480_ASAP15_ctrl_NP16-21_PFC_4"
## [187] "DA432_ASAP12_PD_P74_PFC_4" "MJ_ASAP14_ctrl_NP16-164_PFC_4"
## [189] "ASAP155_ctrl_NP23-21_PFC_4" "DA499_ASAP44_PD_NP19-255_PFC_4"
## [191] "DA490_ASAP11_PD_P73_PFC_4" "DA808_ASAP41_PD_NP19-108_PFC_4"
## [193] "DA804_ASAP49_ctrl_NP18-159_PFC_4" "DA430_ASAP9_PD_NP16-162_PFC_4"
## [195] "AA_ASAP116_PD_NP22-55_PFC_4" "DA795_ASAP55_ctrl_NP19-37_PFC_4"
## [197] "DA476_ASAP10_PD_NP16-25_PFC_4"
##
## $order_rows
## [1] "HERV_dup3363" "HERV_dup2977" "HERV_dup2555" "HERV_dup1948"
## [5] "HERV_dup2809" "HERV_dup1556" "HERV_dup1730" "HERV_dup723"
## [9] "HERV_dup3227" "HERV_dup551" "HERV_dup2879" "HERV_dup369"
## [13] "HERV_dup1303" "HERV_dup1823" "HERV_dup977" "HERV_dup276"
## [17] "HERV_dup3189" "HERV_dup2848" "HERV_dup3507" "HERV_dup3505"
## [21] "HERV_dup2847" "HERV_dup2093" "HERV_dup2743" "HERV_dup2599"
## [25] "HERV_dup2772" "HERV_dup3171" "HERV_dup1272" "HERV_dup851"
## [29] "HERV_dup348" "HERV_dup2319" "HERV_dup1321" "HERV_dup916"
## [33] "HERV_dup1658" "HERV_dup3196" "HERV_dup1036" "HERV_dup508"
## [37] "HERV_dup831" "HERV_dup399" "HERV_dup1208" "HERV_dup1943"
## [41] "HERV_dup2320" "HERV_dup243" "HERV_dup631" "HERV_dup565"
## [45] "HERV_dup336" "HERV_dup1673" "HERV_dup23" "HERV_dup250"
## [49] "HERV_dup2730" "HERV_dup251" "HERV_dup2130" "HERV_dup1520"
## [53] "HERV_dup968" "HERV_dup2907" "HERV_dup1605" "HERV_dup3459"
## [57] "HERV_dup329" "HERV_dup626" "HERV_dup2566" "HERV_dup640"
## [61] "HERV_dup2041" "HERV_dup3694" "HERV_dup2934" "HERV_dup3117"
## [65] "HERV_dup3341" "HERV_dup3328" "HERV_dup2476" "HERV_dup1324"
## [69] "HERV_dup934" "HERV_dup2112" "HERV_dup1447" "HERV_dup1319"
## [73] "HERV_dup202" "HERV_dup203" "HERV_dup990" "HERV_dup2292"
## [77] "HERV_dup218" "HERV_dup2784" "HERV_dup2366" "HERV_dup1362"
## [81] "HERV_dup282" "HERV_dup446" "HERV_dup2941" "HERV_dup2383"
## [85] "HERV_dup1657" "HERV_dup2404" "HERV_dup1891" "HERV_dup1304"
## [89] "HERV_dup2152" "HERV_dup1331" "HERV_dup2939" "HERV_dup1557"
## [93] "HERV_dup1089" "HERV_dup2886" "HERV_dup183" "HERV_dup3044"
## [97] "HERV_dup2557" "HERV_dup1003" "HERV_dup1187" "HERV_dup57"
## [101] "HERV_dup1302" "HERV_dup2655" "HERV_dup1933" "HERV_dup1932"
## [105] "HERV_dup2479" "HERV_dup1757" "HERV_dup2187" "HERV_dup2936"
## [109] "HERV_dup3284" "HERV_dup595" "HERV_dup1440" "HERV_dup1049"
## [113] "HERV_dup133" "HERV_dup471" "HERV_dup1210" "HERV_dup1093"
## [117] "HERV_dup2441" "HERV_dup1438" "HERV_dup398" "HERV_dup400"
## [121] "HERV_dup1415" "HERV_dup3182" "HERV_dup441" "HERV_dup982"
## [125] "HERV_dup1389" "HERV_dup2635" "HERV_dup2536" "HERV_dup1228"
## [129] "HERV_dup2942" "HERV_dup572" "HERV_dup115" "HERV_dup272"
## [133] "HERV_dup467" "HERV_dup2647" "HERV_dup194" "HERV_dup1007"
## [137] "HERV_dup201" "HERV_dup301" "HERV_dup469" "HERV_dup1366"
## [141] "HERV_dup732" "HERV_dup3212" "HERV_dup1245" "HERV_dup2604"
## [145] "HERV_dup736" "HERV_dup1099" "HERV_dup729" "HERV_dup1218"
## [149] "HERV_dup1108" "HERV_dup728" "HERV_dup935" "HERV_dup2264"
## [153] "HERV_dup3154" "HERV_dup1346" "HERV_dup443" "HERV_dup634"
## [157] "HERV_dup381" "HERV_dup517" "HERV_dup344" "HERV_dup1514"
## [161] "HERV_dup1638" "HERV_dup388" "HERV_dup17" "HERV_dup682"
## [165] "HERV_dup530" "HERV_dup1937" "HERV_dup509" "HERV_dup2972"
## [169] "HERV_dup1146" "HERV_dup2823" "HERV_dup735" "HERV_dup772"
## [173] "HERV_dup3215" "HERV_dup2464" "HERV_dup1131" "HERV_dup568"
## [177] "HERV_dup1278" "HERV_dup1668" "HERV_dup1378" "HERV_dup2129"
## [181] "HERV_dup2518" "HERV_dup884" "HERV_dup2481" "HERV_dup1944"
## [185] "HERV_dup1494" "HERV_dup2217" "HERV_dup2602" "HERV_dup1776"
## [189] "HERV_dup556" "HERV_dup1254" "HERV_dup1869" "HERV_dup1931"
## [193] "HERV_dup3408" "HERV_dup2324" "HERV_dup3688" "HERV_dup570"
## [197] "HERV_dup1724" "HERV_dup1639" "HERV_dup2272" "HERV_dup554"
## [201] "HERV_dup184" "HERV_dup3016" "HERV_dup321" "HERV_dup1112"
## [205] "HERV_dup3073" "HERV_dup447" "HERV_dup357" "HERV_dup2034"
## [209] "HERV_dup1273" "HERV_dup1073" "HERV_dup930" "HERV_dup739"
## [213] "HERV_dup3545" "HERV_dup1213" "HERV_dup1958" "HERV_dup314"
## [217] "HERV_dup3607" "HERV_dup461" "HERV_dup519" "HERV_dup29"
## [221] "HERV_dup3481" "HERV_dup3131" "HERV_dup2620" "HERV_dup180"
## [225] "HERV_dup3137" "HERV_dup2747" "HERV_dup177" "HERV_dup966"
## [229] "HERV_dup2141" "HERV_dup3015" "HERV_dup1239" "HERV_dup967"
## [233] "HERV_dup39" "HERV_dup850" "HERV_dup1934" "HERV_dup2945"
## [237] "HERV_dup86" "HERV_dup1295" "HERV_dup2290" "HERV_dup2878"
## [241] "HERV_dup1902" "HERV_dup2603" "HERV_dup2482" "HERV_dup2242"
## [245] "HERV_dup2706" "HERV_dup1374" "HERV_dup3108" "HERV_dup1403"
## [249] "HERV_dup3219" "HERV_dup2033" "HERV_dup1212" "HERV_dup2804"
## [253] "HERV_dup692" "HERV_dup84" "HERV_dup291" "HERV_dup3063"
## [257] "HERV_dup3588" "HERV_dup1279" "HERV_dup1733" "HERV_dup870"
## [261] "HERV_dup3037" "HERV_dup127" "HERV_dup894" "HERV_dup3031"
## [265] "HERV_dup1656" "HERV_dup355" "HERV_dup2797" "HERV_dup3430"
## [269] "HERV_dup662" "HERV_dup3519" "HERV_dup2561" "HERV_dup3406"
## [273] "HERV_dup1979" "HERV_dup1248" "HERV_dup3013" "HERV_dup120"
## [277] "HERV_dup1236" "HERV_dup185" "HERV_dup3319" "HERV_dup1005"
## [281] "HERV_dup3008" "HERV_dup2680" "HERV_dup1555" "HERV_dup591"
## [285] "HERV_dup2128" "HERV_dup1513" "HERV_dup1071" "HERV_dup2356"
## [289] "HERV_dup108" "HERV_dup58" "HERV_dup3416" "HERV_dup1017"
## [293] "HERV_dup1156" "HERV_dup2529" "HERV_dup1532" "HERV_dup3210"
## [297] "HERV_dup2100" "HERV_dup3673" "HERV_dup2857" "HERV_dup2949"
## [301] "HERV_dup924" "HERV_dup1496" "HERV_dup34" "HERV_dup505"
## [305] "HERV_dup2337" "HERV_dup1500" "HERV_dup1047" "HERV_dup1222"
## [309] "HERV_dup389" "HERV_dup2840" "HERV_dup1640" "HERV_dup1541"
## [313] "HERV_dup1655" "HERV_dup1316" "HERV_dup2525" "HERV_dup2278"
## [317] "HERV_dup1253" "HERV_dup2801" "HERV_dup277" "HERV_dup2778"
## [321] "HERV_dup1491" "HERV_dup21" "HERV_dup2548" "HERV_dup2696"
## [325] "HERV_dup1107" "HERV_dup1470" "HERV_dup1923" "HERV_dup3187"
## [329] "HERV_dup1401" "HERV_dup1322" "HERV_dup1661" "HERV_dup1201"
## [333] "HERV_dup1184" "HERV_dup1935" "HERV_dup409" "HERV_dup2027"
## [337] "HERV_dup773" "HERV_dup1052" "HERV_dup975" "HERV_dup488"
## [341] "HERV_dup2646" "HERV_dup1611" "HERV_dup1307" "HERV_dup3358"
## [345] "HERV_dup2533" "HERV_dup1240" "HERV_dup1614" "HERV_dup1339"
## [349] "HERV_dup632" "HERV_dup1755" "HERV_dup703" "HERV_dup487"
## [353] "HERV_dup2334" "HERV_dup2905" "HERV_dup1720" "HERV_dup2530"
## [357] "HERV_dup2562" "HERV_dup882" "HERV_dup2378" "HERV_dup1364"
## [361] "HERV_dup3050" "HERV_dup2480" "HERV_dup1350" "HERV_dup3286"
## [365] "HERV_dup1914" "HERV_dup1804" "HERV_dup933" "HERV_dup5"
## [369] "HERV_dup1390" "HERV_dup2891" "HERV_dup3217" "HERV_dup2159"
## [373] "HERV_dup2663" "HERV_dup2653" "HERV_dup3100" "HERV_dup3394"
## [377] "HERV_dup2843" "HERV_dup3270" "HERV_dup433" "HERV_dup599"
## [381] "HERV_dup1526" "HERV_dup1972" "HERV_dup419" "HERV_dup1356"
## [385] "HERV_dup1653" "HERV_dup1327" "HERV_dup1920" "HERV_dup3366"
## [389] "HERV_dup710" "HERV_dup1459" "HERV_dup746" "HERV_dup981"
## [393] "HERV_dup1064" "HERV_dup577" "HERV_dup665" "HERV_dup876"
## [397] "HERV_dup578" "HERV_dup2415" "HERV_dup1453" "HERV_dup1103"
## [401] "HERV_dup2735" "HERV_dup2728" "HERV_dup586" "HERV_dup1046"
## [405] "HERV_dup1412" "HERV_dup1851" "HERV_dup1629" "HERV_dup2978"
## [409] "HERV_dup2979" "HERV_dup452" "HERV_dup450" "HERV_dup2303"
## [413] "HERV_dup1383" "HERV_dup1962" "HERV_dup3181" "HERV_dup3179"
## [417] "HERV_dup356" "HERV_dup1269" "HERV_dup27" "HERV_dup2250"
## [421] "HERV_dup2632" "HERV_dup1433" "HERV_dup331" "HERV_dup2897"
## [425] "HERV_dup3239" "HERV_dup1926" "HERV_dup3107" "HERV_dup2937"
## [429] "HERV_dup1029" "HERV_dup3140" "HERV_dup1413" "HERV_dup909"
## [433] "HERV_dup2785" "HERV_dup1847" "HERV_dup1846" "HERV_dup2550"
## [437] "HERV_dup1587" "HERV_dup1268" "HERV_dup118" "HERV_dup2967"
## [441] "HERV_dup776" "HERV_dup803" "HERV_dup2149" "HERV_dup1752"
## [445] "HERV_dup724" "HERV_dup3287" "HERV_dup846" "HERV_dup1090"
## [449] "HERV_dup129" "HERV_dup407" "HERV_dup293" "HERV_dup1579"
## [453] "HERV_dup152" "HERV_dup613" "HERV_dup573" "HERV_dup799"
## [457] "HERV_dup2365" "HERV_dup562" "HERV_dup1359" "HERV_dup2900"
## [461] "HERV_dup1050" "HERV_dup386" "HERV_dup214" "HERV_dup3231"
## [465] "HERV_dup899" "HERV_dup1334" "HERV_dup2182" "HERV_dup2736"
## [469] "HERV_dup3148" "HERV_dup1081" "HERV_dup1082" "HERV_dup1717"
## [473] "HERV_dup1285" "HERV_dup112" "HERV_dup2651" "HERV_dup904"
## [477] "HERV_dup1282" "HERV_dup3351" "HERV_dup2963" "HERV_dup1750"
## [481] "HERV_dup1731" "HERV_dup54" "HERV_dup758" "HERV_dup2391"
## [485] "HERV_dup2166" "HERV_dup1662" "HERV_dup434" "HERV_dup1719"
## [489] "HERV_dup900" "HERV_dup3105" "HERV_dup2985" "HERV_dup1333"
## [493] "HERV_dup1114" "HERV_dup2282" "HERV_dup377" "HERV_dup1394"
## [497] "HERV_dup2964" "HERV_dup890" "HERV_dup2855" "HERV_dup1351"
## [501] "HERV_dup2500" "HERV_dup852" "HERV_dup3124" "HERV_dup1868"
## [505] "HERV_dup3522" "HERV_dup1345" "HERV_dup110" "HERV_dup38"
## [509] "HERV_dup2436" "HERV_dup873" "HERV_dup1707" "HERV_dup1381"
## [513] "HERV_dup1048" "HERV_dup300" "HERV_dup1080" "HERV_dup2962"
## [517] "HERV_dup1780" "HERV_dup3220" "HERV_dup151" "HERV_dup1890"
## [521] "HERV_dup2179" "HERV_dup1953" "HERV_dup1235" "HERV_dup956"
## [525] "HERV_dup597" "HERV_dup2631" "HERV_dup2163" "HERV_dup1778"
## [529] "HERV_dup18" "HERV_dup2739" "HERV_dup2607" "HERV_dup1598"
## [533] "HERV_dup1437" "HERV_dup880" "HERV_dup290" "HERV_dup2623"
## [537] "HERV_dup1940" "HERV_dup2803" "HERV_dup2643" "HERV_dup3033"
## [541] "HERV_dup2733" "HERV_dup1243" "HERV_dup94" "HERV_dup980"
## [545] "HERV_dup1298" "HERV_dup1001" "HERV_dup26" "HERV_dup1371"
## [549] "HERV_dup1242" "HERV_dup1663" "HERV_dup2769" "HERV_dup93"
## [553] "HERV_dup2589" "HERV_dup2588" "HERV_dup2896" "HERV_dup1416"
## [557] "HERV_dup1875" "HERV_dup1613" "HERV_dup1195" "HERV_dup350"
## [561] "HERV_dup2422" "HERV_dup3335" "HERV_dup492" "HERV_dup215"
## [565] "HERV_dup3143" "HERV_dup2188" "HERV_dup2183" "HERV_dup380"
## [569] "HERV_dup2273" "HERV_dup2812" "HERV_dup36" "HERV_dup417"
## [573] "HERV_dup1417" "HERV_dup2598" "HERV_dup777" "HERV_dup2299"
## [577] "HERV_dup2298" "HERV_dup1703" "HERV_dup2379" "HERV_dup2834"
## [581] "HERV_dup2002" "HERV_dup1512" "HERV_dup3251" "HERV_dup1617"
## [585] "HERV_dup2353" "HERV_dup3198" "HERV_dup2235" "HERV_dup1569"
## [589] "HERV_dup2012" "HERV_dup949" "HERV_dup3410" "HERV_dup2856"
## [593] "HERV_dup249" "HERV_dup1209" "HERV_dup2966" "HERV_dup1281"
## [597] "HERV_dup1888" "HERV_dup2019" "HERV_dup2877" "HERV_dup1671"
## [601] "HERV_dup1317" "HERV_dup3365" "HERV_dup671" "HERV_dup670"
## [605] "HERV_dup2524" "HERV_dup65" "HERV_dup3118" "HERV_dup3355"
## [609] "HERV_dup3529" "HERV_dup3580" "HERV_dup1982" "HERV_dup2106"
## [613] "HERV_dup2176" "HERV_dup1357" "HERV_dup2085" "HERV_dup1484"
## [617] "HERV_dup3266" "HERV_dup1203" "HERV_dup1694" "HERV_dup1004"
## [621] "HERV_dup1102" "HERV_dup1232" "HERV_dup612" "HERV_dup1756"
## [625] "HERV_dup2915" "HERV_dup1382" "HERV_dup939" "HERV_dup2261"
## [629] "HERV_dup3418" "HERV_dup2695" "HERV_dup1702" "HERV_dup872"
## [633] "HERV_dup2438" "HERV_dup482" "HERV_dup1315" "HERV_dup2111"
## [637] "HERV_dup1596" "HERV_dup1802" "HERV_dup61" "HERV_dup265"
## [641] "HERV_dup3342" "HERV_dup3343" "HERV_dup600" "HERV_dup954"
## [645] "HERV_dup2914" "HERV_dup2961" "HERV_dup2412" "HERV_dup1002"
## [649] "HERV_dup1283" "HERV_dup1973" "HERV_dup927" "HERV_dup1297"
## [653] "HERV_dup1308" "HERV_dup3390" "HERV_dup1889" "HERV_dup1358"
## [657] "HERV_dup2134" "HERV_dup2789" "HERV_dup292" "HERV_dup1"
## [661] "HERV_dup1456" "HERV_dup2376" "HERV_dup474" "HERV_dup2902"
## [665] "HERV_dup468" "HERV_dup470" "HERV_dup3226" "HERV_dup1309"
## [669] "HERV_dup926" "HERV_dup1255" "HERV_dup209" "HERV_dup913"
## [673] "HERV_dup1917" "HERV_dup979" "HERV_dup1749" "HERV_dup3375"
## [677] "HERV_dup302" "HERV_dup1000" "HERV_dup1669" "HERV_dup2841"
## [681] "HERV_dup288" "HERV_dup717" "HERV_dup731" "HERV_dup3423"
## [685] "HERV_dup2491" "HERV_dup1310" "HERV_dup3174" "HERV_dup2662"
## [689] "HERV_dup2752" "HERV_dup3417" "HERV_dup3388" "HERV_dup2266"
## [693] "HERV_dup1670" "HERV_dup37" "HERV_dup384" "HERV_dup2158"
## [697] "HERV_dup3379" "HERV_dup518" "HERV_dup969" "HERV_dup3020"
## [701] "HERV_dup1449" "HERV_dup1708" "HERV_dup1079" "HERV_dup1701"
## [705] "HERV_dup1758" "HERV_dup2381" "HERV_dup3252" "HERV_dup3357"
## [709] "HERV_dup379" "HERV_dup2880" "HERV_dup2838" "HERV_dup940"
## [713] "HERV_dup614" "L1PA3_dup1010" "L1PA3_dup4994" "L1PA3_dup1311"
## [717] "L1PA3_dup2919" "L1PA3_dup2517" "L1PA3_dup8663" "L1PA2_dup1272"
## [721] "L1PA3_dup4888" "L1PA2_dup927" "L1PA2_dup2245" "L1PA3_dup1756"
## [725] "L1PA2_dup922" "L1PA3_dup2593" "L1PA2_dup1230" "L1PA3_dup373"
## [729] "L1PA3_dup529" "L1HS_dup455" "L1PA2_dup410" "L1PA3_dup527"
## [733] "L1PA3_dup2557" "L1PA3_dup4277" "L1PA3_dup6457" "L1PA2_dup848"
## [737] "L1PA3_dup10686" "L1PA3_dup8903" "L1PA3_dup4118" "L1PA3_dup1651"
## [741] "L1PA3_dup1" "L1PA2_dup196" "L1HS_dup240" "L1PA3_dup7862"
## [745] "L1PA3_dup10297" "L1PA2_dup3771" "L1PA2_dup4403" "L1PA3_dup10740"
## [749] "L1HS_dup1462" "L1PA2_dup4620" "L1PA3_dup4349" "L1PA2_dup2271"
## [753] "L1PA3_dup10011" "L1PA3_dup10096" "L1PA2_dup4612" "L1PA2_dup1177"
## [757] "L1PA2_dup98" "L1PA3_dup1647" "L1PA2_dup1968" "L1HS_dup1478"
## [761] "L1PA3_dup5106" "L1PA3_dup3005" "L1PA2_dup684" "L1PA3_dup8313"
## [765] "L1PA2_dup2295" "L1HS_dup811" "L1PA3_dup7947" "L1PA2_dup2047"
## [769] "L1PA3_dup10525" "L1HS_dup907" "L1PA3_dup5594" "L1HS_dup743"
## [773] "L1PA3_dup4259" "L1PA2_dup4421" "L1PA2_dup1023" "L1PA2_dup16"
## [777] "L1PA3_dup6112" "L1PA3_dup1463" "L1PA2_dup4936" "L1PA3_dup6884"
## [781] "L1PA3_dup8896" "L1PA3_dup5358" "L1PA3_dup5355" "L1PA3_dup3763"
## [785] "L1PA3_dup7840" "L1PA2_dup1621" "L1PA2_dup423" "L1PA3_dup3950"
## [789] "L1PA2_dup4043" "L1PA3_dup2683" "L1PA3_dup7432" "L1HS_dup1576"
## [793] "L1PA2_dup949" "L1PA2_dup1978" "L1PA3_dup345" "L1PA2_dup2581"
## [797] "L1PA2_dup1331" "L1PA2_dup3003" "L1HS_dup1324" "L1PA3_dup6160"
## [801] "L1PA2_dup3930" "L1PA2_dup4309" "L1PA3_dup6008" "L1PA3_dup9202"
## [805] "L1PA3_dup9856" "L1PA3_dup3404" "L1PA3_dup2643" "L1PA3_dup3484"
## [809] "L1PA3_dup4393" "L1PA2_dup4226" "L1PA2_dup678" "L1PA3_dup1328"
## [813] "L1HS_dup879" "L1PA2_dup3283" "L1PA3_dup7316" "L1PA3_dup1026"
## [817] "L1PA3_dup1027" "L1PA3_dup7605" "L1PA3_dup5544" "L1HS_dup1357"
## [821] "L1PA2_dup4262" "L1PA3_dup400" "L1PA2_dup2408" "L1PA2_dup4776"
## [825] "L1PA3_dup9722" "L1PA3_dup1337" "L1PA2_dup1653" "L1PA2_dup4045"
## [829] "L1PA2_dup805" "L1HS_dup1019" "L1PA3_dup1264" "L1PA2_dup3881"
## [833] "L1PA3_dup9255" "L1PA2_dup3607" "L1PA3_dup9473" "L1PA2_dup3405"
## [837] "L1PA3_dup4688" "L1PA2_dup1770" "L1PA2_dup4714" "L1PA2_dup4440"
## [841] "L1PA2_dup2969" "L1PA2_dup3622" "L1PA2_dup2343" "L1PA3_dup5418"
## [845] "L1PA2_dup1058" "L1PA3_dup2755" "L1PA2_dup4441" "L1PA2_dup1375"
## [849] "L1HS_dup62" "L1PA2_dup358" "L1PA3_dup10176" "L1HS_dup1005"
## [853] "L1HS_dup995" "L1PA2_dup4901" "L1PA2_dup4618" "L1PA2_dup4237"
## [857] "L1HS_dup1104" "L1PA3_dup6387" "L1PA2_dup747" "L1PA2_dup4688"
## [861] "L1HS_dup35" "L1HS_dup1286" "L1PA2_dup1248" "L1PA2_dup3503"
## [865] "L1PA2_dup514" "L1PA3_dup6436" "L1PA2_dup365" "L1HS_dup679"
## [869] "L1PA3_dup5207" "L1PA3_dup5928" "L1PA3_dup1114" "L1PA2_dup1112"
## [873] "L1PA2_dup2577" "L1PA2_dup4454" "L1PA3_dup10531" "L1PA3_dup8506"
## [877] "L1PA3_dup8117" "L1PA2_dup4335" "L1PA2_dup1463" "L1PA2_dup1476"
## [881] "L1HS_dup143" "L1HS_dup225" "L1PA2_dup383" "L1PA2_dup4686"
## [885] "L1PA2_dup1078" "L1PA2_dup3445" "L1PA2_dup2089" "L1PA3_dup5866"
## [889] "L1PA2_dup1426" "L1PA3_dup10043" "L1HS_dup600" "L1HS_dup579"
## [893] "L1HS_dup1393" "L1PA2_dup2180" "L1PA2_dup4389" "L1PA2_dup1490"
## [897] "L1PA2_dup2004" "L1PA2_dup732" "L1HS_dup1077" "L1PA3_dup3291"
## [901] "L1PA2_dup935" "L1HS_dup1243" "L1HS_dup649" "L1PA2_dup4762"
## [905] "L1HS_dup270" "L1PA3_dup1279" "L1PA3_dup2389" "L1PA3_dup5057"
## [909] "L1HS_dup622" "L1PA3_dup3153" "L1PA3_dup6871" "L1HS_dup1020"
## [913] "L1PA2_dup2506" "L1PA2_dup4201" "L1PA2_dup2261" "L1PA2_dup2565"
## [917] "L1PA3_dup9702" "L1HS_dup244" "L1PA2_dup759" "L1PA2_dup3776"
## [921] "L1PA3_dup1046" "L1HS_dup111" "L1PA2_dup4528" "L1PA3_dup5886"
## [925] "L1PA2_dup4196" "L1PA2_dup4639" "L1PA2_dup2504" "L1HS_dup1514"
## [929] "L1PA3_dup247" "L1HS_dup787" "L1HS_dup163" "L1PA3_dup5363"
## [933] "L1PA3_dup638" "L1PA2_dup109" "L1PA2_dup4430" "L1PA2_dup798"
## [937] "L1PA3_dup2620" "L1HS_dup803" "L1HS_dup87" "L1HS_dup1339"
## [941] "L1PA3_dup3684" "L1PA2_dup4548" "L1PA3_dup8891" "L1PA2_dup1398"
## [945] "L1PA2_dup3766" "L1PA2_dup3160" "L1HS_dup1014" "L1PA2_dup2876"
## [949] "L1PA3_dup9866" "L1HS_dup1437" "L1PA3_dup5825" "L1HS_dup376"
## [953] "L1PA2_dup4791" "L1PA2_dup2127" "L1HS_dup1501" "L1PA3_dup1727"
## [957] "L1PA2_dup3426" "L1HS_dup444" "L1PA2_dup589" "L1PA2_dup4432"
## [961] "L1PA2_dup2537" "L1PA3_dup5540" "L1PA3_dup6692" "L1PA2_dup4522"
## [965] "L1PA2_dup4713" "L1PA2_dup4478" "L1PA3_dup7288" "L1PA2_dup4611"
## [969] "L1HS_dup370" "L1HS_dup1342" "L1PA2_dup472" "L1PA2_dup2444"
## [973] "L1PA3_dup840" "L1PA2_dup4652" "L1PA3_dup4687" "L1HS_dup429"
## [977] "L1HS_dup466" "L1HS_dup1284" "L1PA2_dup726" "L1PA3_dup683"
## [981] "L1PA3_dup1943" "L1PA3_dup3959" "L1HS_dup1616" "L1PA2_dup2436"
## [985] "L1HS_dup802" "L1PA2_dup382" "L1HS_dup1491" "L1PA2_dup3118"
## [989] "L1PA2_dup1049" "L1HS_dup204" "L1PA3_dup6523" "L1PA2_dup1992"
## [993] "L1HS_dup1473" "L1PA2_dup3439" "L1PA2_dup3629" "L1PA2_dup307"
## [997] "L1PA2_dup629" "L1PA3_dup5927" "L1PA2_dup4378" "L1PA3_dup1989"
## [1001] "L1PA2_dup360" "L1PA3_dup7893" "L1PA2_dup2168" "L1PA2_dup2282"
## [1005] "L1PA2_dup219" "L1PA3_dup9840" "L1PA2_dup1050" "L1HS_dup90"
## [1009] "L1PA2_dup2729" "L1PA3_dup3586" "L1HS_dup1295" "L1PA2_dup71"
## [1013] "L1PA3_dup165" "L1PA2_dup142" "L1PA3_dup5238" "L1PA2_dup413"
## [1017] "L1PA3_dup978" "L1PA2_dup1933" "L1PA3_dup2357" "L1PA3_dup3954"
## [1021] "L1PA3_dup6317" "L1PA3_dup358" "L1PA3_dup1547" "L1PA2_dup2155"
## [1025] "L1PA3_dup1269" "L1PA3_dup7550" "L1PA3_dup5534" "L1PA2_dup1953"
## [1029] "L1PA3_dup3968" "L1PA2_dup1805" "L1PA2_dup4030" "L1PA3_dup8310"
## [1033] "L1PA3_dup4708" "L1PA3_dup9256" "L1PA2_dup663" "L1PA2_dup526"
## [1037] "L1PA2_dup1418" "L1PA3_dup4709" "L1PA3_dup1800" "L1PA2_dup1778"
## [1041] "L1PA3_dup5514" "L1PA3_dup5121" "L1PA3_dup3758" "L1PA3_dup3757"
## [1045] "L1PA2_dup2289" "L1PA3_dup4902" "L1PA3_dup1723" "L1HS_dup632"
## [1049] "L1HS_dup1536" "L1PA3_dup3306" "L1PA2_dup3742" "L1PA3_dup1952"
## [1053] "L1HS_dup155" "L1HS_dup948" "L1PA3_dup5047" "L1PA2_dup39"
## [1057] "L1PA3_dup3300" "L1PA2_dup1760" "L1PA3_dup3880" "L1PA3_dup4408"
## [1061] "L1HS_dup596" "L1PA3_dup5745" "L1PA2_dup3042" "L1PA3_dup6730"
## [1065] "L1PA2_dup737" "L1PA2_dup741" "L1PA3_dup4596" "L1PA2_dup595"
## [1069] "L1PA3_dup2662" "L1PA2_dup2496" "L1PA2_dup4053" "L1PA3_dup9373"
## [1073] "L1PA2_dup675" "L1PA3_dup9734" "L1HS_dup1182" "L1PA3_dup6929"
## [1077] "L1PA3_dup10072" "L1PA2_dup3425" "L1PA3_dup3729" "L1PA3_dup3323"
## [1081] "L1PA3_dup9946" "L1PA3_dup3102" "L1PA2_dup2385" "L1PA3_dup4603"
## [1085] "L1PA3_dup2204" "L1PA3_dup8520" "L1PA3_dup8872" "L1PA3_dup3863"
## [1089] "L1HS_dup449" "L1PA3_dup1428" "L1PA3_dup5510" "L1PA3_dup8420"
## [1093] "L1PA2_dup3773" "L1PA2_dup4074" "L1PA3_dup1770" "L1HS_dup124"
## [1097] "L1PA2_dup1560" "L1PA3_dup8173" "L1PA2_dup585" "L1PA2_dup2680"
## [1101] "L1PA3_dup2760" "L1PA2_dup2720" "L1PA2_dup662" "L1PA2_dup4596"
## [1105] "L1PA3_dup4487" "L1PA3_dup9430" "L1PA3_dup1988" "L1PA3_dup8571"
## [1109] "L1PA3_dup3307" "L1PA2_dup4838" "L1PA2_dup513" "L1PA3_dup2721"
## [1113] "L1PA3_dup6147" "L1PA3_dup6573" "L1PA2_dup4775" "L1HS_dup916"
## [1117] "L1PA3_dup6584" "L1PA3_dup2954" "L1PA2_dup1749" "L1PA3_dup4804"
## [1121] "L1PA3_dup4884" "L1PA3_dup4885" "L1PA3_dup872" "L1PA3_dup2039"
## [1125] "L1PA3_dup761" "L1PA3_dup7237" "L1PA3_dup4391" "L1PA2_dup3805"
## [1129] "L1PA2_dup3589" "L1PA3_dup3507" "L1PA2_dup200" "L1PA3_dup3168"
## [1133] "L1PA3_dup7821" "L1PA3_dup1710" "L1PA2_dup1298" "L1PA3_dup7472"
## [1137] "L1PA3_dup4891" "L1PA3_dup7963" "L1PA3_dup4401" "L1PA3_dup7951"
## [1141] "L1PA2_dup3736" "L1PA2_dup2909" "L1HS_dup1330" "L1PA3_dup6002"
## [1145] "L1PA2_dup221" "L1PA3_dup10285" "L1PA3_dup3941" "L1PA2_dup635"
## [1149] "L1PA3_dup6385" "L1PA3_dup2272" "L1HS_dup191" "L1PA2_dup1752"
## [1153] "L1PA2_dup559" "L1PA2_dup2860" "L1HS_dup514" "L1PA3_dup6434"
## [1157] "L1PA3_dup9280" "L1PA3_dup561" "L1PA2_dup2164" "L1HS_dup788"
## [1161] "L1PA2_dup1462" "L1PA2_dup1379" "L1PA3_dup5680" "L1PA2_dup791"
## [1165] "L1PA3_dup10119" "L1PA3_dup8525" "L1PA2_dup2988" "L1PA3_dup7864"
## [1169] "L1HS_dup138" "L1PA3_dup7470" "L1PA2_dup3531" "L1PA2_dup234"
## [1173] "L1PA3_dup8007" "L1PA3_dup9998" "L1PA2_dup130" "L1PA3_dup5337"
## [1177] "L1HS_dup831" "L1PA3_dup1528" "L1PA3_dup10344" "L1PA3_dup8522"
## [1181] "L1PA2_dup3292" "L1PA2_dup3615" "L1HS_dup379" "L1PA2_dup4651"
## [1185] "L1PA3_dup8328" "L1PA3_dup6966" "L1PA3_dup3502" "L1PA2_dup1746"
## [1189] "L1PA3_dup6347" "L1PA2_dup3136" "L1HS_dup405" "L1PA2_dup2863"
## [1193] "L1PA3_dup1554" "L1PA2_dup326" "L1PA3_dup3509" "L1PA2_dup994"
## [1197] "L1PA2_dup2430" "L1PA3_dup5468" "L1PA2_dup2254" "L1PA2_dup3484"
## [1201] "L1PA2_dup727" "L1PA2_dup3579" "L1PA3_dup1550" "L1PA3_dup4668"
## [1205] "L1PA3_dup7792" "L1PA3_dup2393" "L1PA2_dup3437" "L1PA3_dup9095"
## [1209] "L1PA3_dup1937" "L1PA2_dup4367" "L1PA3_dup128" "L1PA3_dup124"
## [1213] "L1PA2_dup2791" "L1PA3_dup7637" "L1PA3_dup4122" "L1PA3_dup907"
## [1217] "L1HS_dup337" "L1PA3_dup6036" "L1PA2_dup4905" "L1PA3_dup2551"
## [1221] "L1PA2_dup2091" "L1PA3_dup398" "L1PA2_dup378" "L1PA2_dup530"
## [1225] "L1PA3_dup2744" "L1PA3_dup9021" "L1PA2_dup3664" "L1PA2_dup37"
## [1229] "L1HS_dup800" "L1PA3_dup6550" "L1PA3_dup748" "L1PA3_dup4492"
## [1233] "L1PA3_dup2413"
asap_heatmap_snRNA(region = c("PUT"),
tes = data_TE_annotation$TE_id,
return_df = F, group_rows = c("type"), gaps_row = length(heatmap_put_HERV_order),
breaks = seq(0,15,length.out = 52), index_row_reorder = c(heatmap_put_HERV_order,heatmap_put_L1_order),
order_cols_groups = order_cols_celltype,
data = TE_data, group_cols = c("celltype"),
title = "PUT HERVs + L1s: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
exclude_clusters = c(6, 7))

## $heatmap
##
## $order_cols
## [1] "AA82_ASAP68_PD_NP18-117_PUT_0" "AA_ASAP98_ctrl_NP16-119_PUT_0"
## [3] "AA_ASAP138_PD_NP16-285_PUT_0" "AA79_ASAP64_PD_NP16-162_PUT_0"
## [5] "AA71_ASAP70_PD_NP18-304_PUT_0" "AA_ASAP141_ctrl_NP19-218_PUT_0"
## [7] "AA_ASAP97_PD_NP21-57_PUT_0" "AA_ASAP100_ctrl_NP18-148_PUT_0"
## [9] "AA84_ASAP71_PD_NP19-16_PUT_0" "AA87_ASAP76_ctrl_NP18-159_PUT_0"
## [11] "AA74_ASAP62_PD_NP16-140_PUT_0" "AA84_ASAP71_PD_NP19-16_PUT_1"
## [13] "AA71_ASAP70_PD_NP18-304_PUT_1" "AA_ASAP100_ctrl_NP18-148_PUT_1"
## [15] "AA79_ASAP64_PD_NP16-162_PUT_1" "AA87_ASAP76_ctrl_NP18-159_PUT_1"
## [17] "AA74_ASAP62_PD_NP16-140_PUT_1" "AA_ASAP139_PD_NP17-232_PUT_1"
## [19] "AA_ASAP144_PD_NP19-137_PUT_1" "AA_ASAP92_ctrl_NP16-284_PUT_1"
## [21] "AA_ASAP117_PD_NP22-55_PUT_1" "AA_ASAP87_PD_NP21-208_PUT_1"
## [23] "AA_ASAP88_PD_NP21-217_PUT_1" "AA_ASAP88_PD_NP21-217_PUT_2"
## [25] "AA85_ASAP72_PD_NP19-23_PUT_2" "AA73_ASAP65_PD_NP16-269_PUT_2"
## [27] "AA82_ASAP68_PD_NP18-117_PUT_2" "AA86_ASAP73_PD_NP19-108_PUT_2"
## [29] "AA_ASAP144_PD_NP19-137_PUT_2" "AA79_ASAP64_PD_NP16-162_PUT_2"
## [31] "AA_ASAP117_PD_NP22-55_PUT_2" "AA83_ASAP69_PD_NP18-287_PUT_2"
## [33] "AA81_ASAP67_PD_NP17-191_PUT_2" "AA77_ASAP61_PD_NP16-25_PUT_2"
## [35] "AA_ASAP140_PD_NP19-91_PUT_2" "AA_ASAP141_ctrl_NP19-218_PUT_2"
## [37] "AA76_ASAP74_PD_NP19-255_PUT_2" "AA_ASAP96_ctrl_NP18-46_PUT_2"
## [39] "AA88_ASAP77_ctrl_NP19-36_PUT_2" "AA89_ASAP78_ctrl_NP19-37_PUT_2"
## [41] "AA_ASAP94_ctrl_NP17-20_PUT_2" "AA_ASAP139_PD_NP17-232_PUT_2"
## [43] "AA_ASAP93_ctrl_NP16-293_PUT_2" "AA71_ASAP70_PD_NP18-304_PUT_2"
## [45] "AA74_ASAP62_PD_NP16-140_PUT_2" "AA_ASAP87_PD_NP21-208_PUT_2"
## [47] "AA_ASAP97_PD_NP21-57_PUT_2" "AA84_ASAP71_PD_NP19-16_PUT_2"
## [49] "AA87_ASAP76_ctrl_NP18-159_PUT_2" "AA_ASAP100_ctrl_NP18-148_PUT_2"
## [51] "AA_ASAP138_PD_NP16-285_PUT_2" "AA_ASAP98_ctrl_NP16-119_PUT_2"
## [53] "AA_ASAP92_ctrl_NP16-284_PUT_2" "AA_ASAP146_PD_NP21-04_PUT_2"
## [55] "AA_ASAP139_PD_NP17-232_PUT_3" "AA_ASAP117_PD_NP22-55_PUT_3"
## [57] "AA_ASAP138_PD_NP16-285_PUT_3" "AA79_ASAP64_PD_NP16-162_PUT_3"
## [59] "AA_ASAP100_ctrl_NP18-148_PUT_3" "AA_ASAP141_ctrl_NP19-218_PUT_3"
## [61] "AA_ASAP144_PD_NP19-137_PUT_3" "AA84_ASAP71_PD_NP19-16_PUT_3"
## [63] "AA_ASAP97_PD_NP21-57_PUT_3" "AA87_ASAP76_ctrl_NP18-159_PUT_3"
## [65] "AA85_ASAP72_PD_NP19-23_PUT_3" "AA88_ASAP77_ctrl_NP19-36_PUT_3"
## [67] "AA_ASAP140_PD_NP19-91_PUT_3" "AA_ASAP142_ctrl_NP22-37_PUT_3"
## [69] "AA86_ASAP73_PD_NP19-108_PUT_3" "AA74_ASAP62_PD_NP16-140_PUT_3"
## [71] "AA_ASAP93_ctrl_NP16-293_PUT_3" "AA_ASAP149_PD_NP23-21_PUT_3"
## [73] "AA89_ASAP78_ctrl_NP19-37_PUT_3" "AA_ASAP146_PD_NP21-04_PUT_3"
## [75] "AA76_ASAP74_PD_NP19-255_PUT_3" "AA83_ASAP69_PD_NP18-287_PUT_3"
## [77] "AA_ASAP87_PD_NP21-208_PUT_3" "AA_ASAP98_ctrl_NP16-119_PUT_3"
## [79] "AA_ASAP96_ctrl_NP18-46_PUT_3" "AA_ASAP88_PD_NP21-217_PUT_3"
## [81] "AA82_ASAP68_PD_NP18-117_PUT_3" "AA73_ASAP65_PD_NP16-269_PUT_3"
## [83] "AA81_ASAP67_PD_NP17-191_PUT_3" "AA71_ASAP70_PD_NP18-304_PUT_3"
## [85] "AA77_ASAP61_PD_NP16-25_PUT_3" "AA_ASAP94_ctrl_NP17-20_PUT_3"
## [87] "AA_ASAP92_ctrl_NP16-284_PUT_3" "AA_ASAP92_ctrl_NP16-284_PUT_5"
## [89] "AA78_ASAP63_PD_NP16-160_PUT_5" "AA_ASAP149_PD_NP23-21_PUT_5"
## [91] "AA76_ASAP74_PD_NP19-255_PUT_5" "AA_ASAP142_ctrl_NP22-37_PUT_5"
## [93] "AA_ASAP93_ctrl_NP16-293_PUT_5" "AA85_ASAP72_PD_NP19-23_PUT_5"
## [95] "AA_ASAP88_PD_NP21-217_PUT_5" "AA88_ASAP77_ctrl_NP19-36_PUT_5"
## [97] "AA_ASAP98_ctrl_NP16-119_PUT_5" "AA74_ASAP62_PD_NP16-140_PUT_5"
## [99] "AA82_ASAP68_PD_NP18-117_PUT_5" "AA73_ASAP65_PD_NP16-269_PUT_5"
## [101] "AA_ASAP146_PD_NP21-04_PUT_5" "AA89_ASAP78_ctrl_NP19-37_PUT_5"
## [103] "AA_ASAP96_ctrl_NP18-46_PUT_5" "AA_ASAP117_PD_NP22-55_PUT_5"
## [105] "AA79_ASAP64_PD_NP16-162_PUT_5" "AA_ASAP94_ctrl_NP17-20_PUT_5"
## [107] "AA86_ASAP73_PD_NP19-108_PUT_5" "AA71_ASAP70_PD_NP18-304_PUT_5"
## [109] "AA_ASAP139_PD_NP17-232_PUT_5" "AA_ASAP138_PD_NP16-285_PUT_5"
## [111] "AA_ASAP140_PD_NP19-91_PUT_5" "AA_ASAP144_PD_NP19-137_PUT_5"
## [113] "AA_ASAP87_PD_NP21-208_PUT_5" "AA84_ASAP71_PD_NP19-16_PUT_5"
## [115] "AA_ASAP141_ctrl_NP19-218_PUT_5" "AA_ASAP100_ctrl_NP18-148_PUT_5"
## [117] "AA87_ASAP76_ctrl_NP18-159_PUT_5" "AA_ASAP97_PD_NP21-57_PUT_5"
## [119] "AA81_ASAP67_PD_NP17-191_PUT_5" "AA83_ASAP69_PD_NP18-287_PUT_5"
## [121] "AA77_ASAP61_PD_NP16-25_PUT_5" "AA89_ASAP78_ctrl_NP19-37_PUT_4"
## [123] "AA_ASAP94_ctrl_NP17-20_PUT_4" "AA_ASAP96_ctrl_NP18-46_PUT_4"
## [125] "AA_ASAP138_PD_NP16-285_PUT_4" "AA_ASAP141_ctrl_NP19-218_PUT_4"
## [127] "AA_ASAP140_PD_NP19-91_PUT_4" "AA79_ASAP64_PD_NP16-162_PUT_4"
## [129] "AA76_ASAP74_PD_NP19-255_PUT_4" "AA77_ASAP61_PD_NP16-25_PUT_4"
## [131] "AA73_ASAP65_PD_NP16-269_PUT_4" "AA_ASAP88_PD_NP21-217_PUT_4"
## [133] "AA85_ASAP72_PD_NP19-23_PUT_4" "AA_ASAP117_PD_NP22-55_PUT_4"
## [135] "AA_ASAP98_ctrl_NP16-119_PUT_4" "AA_ASAP87_PD_NP21-208_PUT_4"
## [137] "AA84_ASAP71_PD_NP19-16_PUT_4" "AA_ASAP144_PD_NP19-137_PUT_4"
## [139] "AA_ASAP100_ctrl_NP18-148_PUT_4" "AA87_ASAP76_ctrl_NP18-159_PUT_4"
## [141] "AA_ASAP97_PD_NP21-57_PUT_4" "AA71_ASAP70_PD_NP18-304_PUT_4"
## [143] "AA83_ASAP69_PD_NP18-287_PUT_4" "AA81_ASAP67_PD_NP17-191_PUT_4"
## [145] "AA74_ASAP62_PD_NP16-140_PUT_4"
##
## $order_rows
## [1] "HERV_dup940" "HERV_dup3357" "HERV_dup379" "HERV_dup1758"
## [5] "HERV_dup1079" "HERV_dup1708" "HERV_dup2880" "HERV_dup2381"
## [9] "HERV_dup3375" "HERV_dup2838" "HERV_dup3423" "HERV_dup731"
## [13] "HERV_dup1669" "HERV_dup1000" "HERV_dup1701" "HERV_dup2841"
## [17] "HERV_dup288" "HERV_dup3174" "HERV_dup2491" "HERV_dup2662"
## [21] "HERV_dup474" "HERV_dup979" "HERV_dup209" "HERV_dup1749"
## [25] "HERV_dup926" "HERV_dup3226" "HERV_dup2158" "HERV_dup1670"
## [29] "HERV_dup518" "HERV_dup37" "HERV_dup1309" "HERV_dup2266"
## [33] "HERV_dup384" "HERV_dup614" "HERV_dup3252" "HERV_dup3379"
## [37] "HERV_dup1310" "HERV_dup2752" "HERV_dup1362" "HERV_dup1359"
## [41] "HERV_dup2847" "HERV_dup2093" "HERV_dup562" "HERV_dup2365"
## [45] "HERV_dup202" "HERV_dup2784" "HERV_dup218" "HERV_dup282"
## [49] "HERV_dup916" "HERV_dup2366" "HERV_dup2292" "HERV_dup194"
## [53] "HERV_dup441" "HERV_dup115" "HERV_dup446" "HERV_dup272"
## [57] "HERV_dup1007" "HERV_dup3355" "HERV_dup3118" "HERV_dup1598"
## [61] "HERV_dup1437" "HERV_dup2607" "HERV_dup18" "HERV_dup852"
## [65] "HERV_dup2353" "HERV_dup380" "HERV_dup398" "HERV_dup215"
## [69] "HERV_dup133" "HERV_dup1943" "HERV_dup876" "HERV_dup1036"
## [73] "HERV_dup492" "HERV_dup2599" "HERV_dup243" "HERV_dup1752"
## [77] "HERV_dup400" "HERV_dup3179" "HERV_dup1195" "HERV_dup2879"
## [81] "HERV_dup3335" "HERV_dup1948" "HERV_dup565" "HERV_dup1440"
## [85] "HERV_dup369" "HERV_dup2743" "HERV_dup1416" "HERV_dup3363"
## [89] "HERV_dup1272" "HERV_dup3181" "HERV_dup2250" "HERV_dup2785"
## [93] "HERV_dup2964" "HERV_dup3143" "HERV_dup3171" "HERV_dup1730"
## [97] "HERV_dup2320" "HERV_dup487" "HERV_dup1089" "HERV_dup1653"
## [101] "HERV_dup573" "HERV_dup409" "HERV_dup1208" "HERV_dup758"
## [105] "HERV_dup2188" "HERV_dup1875" "HERV_dup350" "HERV_dup2422"
## [109] "HERV_dup1322" "HERV_dup377" "HERV_dup890" "HERV_dup1351"
## [113] "HERV_dup1282" "HERV_dup3124" "HERV_dup2963" "HERV_dup2273"
## [117] "HERV_dup1417" "HERV_dup1953" "HERV_dup2733" "HERV_dup1569"
## [121] "HERV_dup1334" "HERV_dup1731" "HERV_dup2166" "HERV_dup899"
## [125] "HERV_dup2235" "HERV_dup1285" "HERV_dup386" "HERV_dup3231"
## [129] "HERV_dup2900" "HERV_dup2736" "HERV_dup1050" "HERV_dup2905"
## [133] "HERV_dup851" "HERV_dup1717" "HERV_dup3148" "HERV_dup1339"
## [137] "HERV_dup2334" "HERV_dup3522" "HERV_dup300" "HERV_dup904"
## [141] "HERV_dup2651" "HERV_dup1114" "HERV_dup1048" "HERV_dup2985"
## [145] "HERV_dup1394" "HERV_dup2319" "HERV_dup2962" "HERV_dup2772"
## [149] "HERV_dup3105" "HERV_dup1613" "HERV_dup1333" "HERV_dup900"
## [153] "HERV_dup1433" "HERV_dup3580" "HERV_dup2848" "HERV_dup2855"
## [157] "HERV_dup3287" "HERV_dup2027" "HERV_dup1052" "HERV_dup3358"
## [161] "HERV_dup1755" "HERV_dup1082" "HERV_dup1081" "HERV_dup2937"
## [165] "HERV_dup2149" "HERV_dup773" "HERV_dup1804" "HERV_dup1090"
## [169] "HERV_dup2646" "HERV_dup1298" "HERV_dup1242" "HERV_dup151"
## [173] "HERV_dup2179" "HERV_dup2834" "HERV_dup1890" "HERV_dup1236"
## [177] "HERV_dup1345" "HERV_dup38" "HERV_dup2533" "HERV_dup2163"
## [181] "HERV_dup3406" "HERV_dup2436" "HERV_dup276" "HERV_dup2404"
## [185] "HERV_dup1657" "HERV_dup1556" "HERV_dup1658" "HERV_dup1662"
## [189] "HERV_dup1611" "HERV_dup301" "HERV_dup799" "HERV_dup2525"
## [193] "HERV_dup1321" "HERV_dup2942" "HERV_dup2383" "HERV_dup2941"
## [197] "HERV_dup1381" "HERV_dup2152" "HERV_dup3505" "HERV_dup3507"
## [201] "HERV_dup882" "HERV_dup2536" "HERV_dup3270" "HERV_dup2480"
## [205] "HERV_dup803" "HERV_dup21" "HERV_dup86" "HERV_dup930"
## [209] "HERV_dup735" "HERV_dup1851" "HERV_dup336" "HERV_dup23"
## [213] "HERV_dup3196" "HERV_dup1273" "HERV_dup2482" "HERV_dup2034"
## [217] "HERV_dup631" "HERV_dup2809" "HERV_dup2977" "HERV_dup723"
## [221] "HERV_dup2183" "HERV_dup399" "HERV_dup348" "HERV_dup831"
## [225] "HERV_dup2555" "HERV_dup3050" "HERV_dup344" "HERV_dup2130"
## [229] "HERV_dup356" "HERV_dup977" "HERV_dup1555" "HERV_dup982"
## [233] "HERV_dup2972" "HERV_dup251" "HERV_dup3227" "HERV_dup551"
## [237] "HERV_dup2562" "HERV_dup1526" "HERV_dup110" "HERV_dup1778"
## [241] "HERV_dup3013" "HERV_dup1248" "HERV_dup1331" "HERV_dup3031"
## [245] "HERV_dup2663" "HERV_dup2653" "HERV_dup2278" "HERV_dup2897"
## [249] "HERV_dup1071" "HERV_dup3694" "HERV_dup1605" "HERV_dup1390"
## [253] "HERV_dup517" "HERV_dup3328" "HERV_dup2356" "HERV_dup1108"
## [257] "HERV_dup2264" "HERV_dup2033" "HERV_dup3416" "HERV_dup2566"
## [261] "HERV_dup3117" "HERV_dup108" "HERV_dup870" "HERV_dup1279"
## [265] "HERV_dup58" "HERV_dup968" "HERV_dup3239" "HERV_dup152"
## [269] "HERV_dup724" "HERV_dup776" "HERV_dup1520" "HERV_dup613"
## [273] "HERV_dup554" "HERV_dup846" "HERV_dup331" "HERV_dup1926"
## [277] "HERV_dup1304" "HERV_dup2632" "HERV_dup1107" "HERV_dup2797"
## [281] "HERV_dup3187" "HERV_dup3286" "HERV_dup599" "HERV_dup127"
## [285] "HERV_dup1099" "HERV_dup5" "HERV_dup2801" "HERV_dup1253"
## [289] "HERV_dup2778" "HERV_dup27" "HERV_dup1720" "HERV_dup1269"
## [293] "HERV_dup2635" "HERV_dup2391" "HERV_dup3100" "HERV_dup662"
## [297] "HERV_dup1356" "HERV_dup1222" "HERV_dup2843" "HERV_dup3366"
## [301] "HERV_dup3140" "HERV_dup1346" "HERV_dup1156" "HERV_dup1029"
## [305] "HERV_dup129" "HERV_dup118" "HERV_dup407" "HERV_dup34"
## [309] "HERV_dup1245" "HERV_dup1366" "HERV_dup293" "HERV_dup1587"
## [313] "HERV_dup1891" "HERV_dup1268" "HERV_dup1412" "HERV_dup1579"
## [317] "HERV_dup1920" "HERV_dup3519" "HERV_dup1047" "HERV_dup1005"
## [321] "HERV_dup1532" "HERV_dup2967" "HERV_dup433" "HERV_dup1184"
## [325] "HERV_dup1972" "HERV_dup1364" "HERV_dup381" "HERV_dup3394"
## [329] "HERV_dup17" "HERV_dup3037" "HERV_dup120" "HERV_dup1962"
## [333] "HERV_dup3430" "HERV_dup2290" "HERV_dup2529" "HERV_dup2804"
## [337] "HERV_dup1979" "HERV_dup1640" "HERV_dup1656" "HERV_dup3189"
## [341] "HERV_dup2378" "HERV_dup1757" "HERV_dup3182" "HERV_dup240"
## [345] "HERV_dup2481" "HERV_dup2823" "HERV_dup2936" "HERV_dup924"
## [349] "HERV_dup1384" "HERV_dup3545" "HERV_dup1103" "HERV_dup3137"
## [353] "HERV_dup2647" "HERV_dup1131" "HERV_dup3044" "HERV_dup2939"
## [357] "HERV_dup1210" "HERV_dup1093" "HERV_dup2680" "HERV_dup2875"
## [361] "HERV_dup3607" "HERV_dup1295" "HERV_dup1187" "HERV_dup1218"
## [365] "HERV_dup2735" "HERV_dup250" "HERV_dup710" "HERV_dup732"
## [369] "HERV_dup578" "HERV_dup591" "HERV_dup1327" "HERV_dup1733"
## [373] "HERV_dup1302" "HERV_dup1046" "HERV_dup1350" "HERV_dup2728"
## [377] "HERV_dup1415" "HERV_dup1557" "HERV_dup746" "HERV_dup3154"
## [381] "HERV_dup586" "HERV_dup2415" "HERV_dup577" "HERV_dup736"
## [385] "HERV_dup3588" "HERV_dup1513" "HERV_dup728" "HERV_dup2907"
## [389] "HERV_dup2878" "HERV_dup772" "HERV_dup2604" "HERV_dup3673"
## [393] "HERV_dup572" "HERV_dup355" "HERV_dup1438" "HERV_dup2840"
## [397] "HERV_dup1378" "HERV_dup39" "HERV_dup1629" "HERV_dup201"
## [401] "HERV_dup2187" "HERV_dup729" "HERV_dup3319" "HERV_dup2886"
## [405] "HERV_dup2464" "HERV_dup1389" "HERV_dup2696" "HERV_dup665"
## [409] "HERV_dup3008" "HERV_dup3108" "HERV_dup1668" "HERV_dup2945"
## [413] "HERV_dup2303" "HERV_dup443" "HERV_dup2242" "HERV_dup3284"
## [417] "HERV_dup935" "HERV_dup57" "HERV_dup1902" "HERV_dup981"
## [421] "HERV_dup1228" "HERV_dup2620" "HERV_dup84" "HERV_dup508"
## [425] "HERV_dup739" "HERV_dup469" "HERV_dup682" "HERV_dup966"
## [429] "HERV_dup1514" "HERV_dup177" "HERV_dup2603" "HERV_dup1278"
## [433] "HERV_dup183" "HERV_dup692" "HERV_dup29" "HERV_dup2548"
## [437] "HERV_dup2857" "HERV_dup634" "HERV_dup2747" "HERV_dup388"
## [441] "HERV_dup2706" "HERV_dup1933" "HERV_dup1932" "HERV_dup1212"
## [445] "HERV_dup1112" "HERV_dup1500" "HERV_dup556" "HERV_dup2949"
## [449] "HERV_dup467" "HERV_dup184" "HERV_dup1638" "HERV_dup1931"
## [453] "HERV_dup1073" "HERV_dup1146" "HERV_dup1017" "HERV_dup2141"
## [457] "HERV_dup2324" "HERV_dup2518" "HERV_dup2100" "HERV_dup1049"
## [461] "HERV_dup530" "HERV_dup3248" "HERV_dup595" "HERV_dup78"
## [465] "HERV_dup661" "HERV_dup2655" "HERV_dup3688" "HERV_dup1491"
## [469] "HERV_dup3219" "HERV_dup2337" "HERV_dup1639" "HERV_dup1403"
## [473] "HERV_dup2272" "HERV_dup3481" "HERV_dup1453" "HERV_dup850"
## [477] "HERV_dup570" "HERV_dup1673" "HERV_dup180" "HERV_dup2441"
## [481] "HERV_dup1823" "HERV_dup3073" "HERV_dup2129" "HERV_dup314"
## [485] "HERV_dup450" "HERV_dup1213" "HERV_dup321" "HERV_dup2217"
## [489] "HERV_dup357" "HERV_dup1239" "HERV_dup2730" "HERV_dup1934"
## [493] "HERV_dup1374" "HERV_dup2192" "HERV_dup3408" "HERV_dup2602"
## [497] "HERV_dup1958" "HERV_dup1172" "HERV_dup3131" "HERV_dup1496"
## [501] "HERV_dup3063" "HERV_dup3015" "HERV_dup519" "HERV_dup3016"
## [505] "HERV_dup1003" "HERV_dup568" "HERV_dup185" "HERV_dup3606"
## [509] "HERV_dup471" "HERV_dup389" "HERV_dup2128" "HERV_dup3217"
## [513] "HERV_dup3210" "HERV_dup2561" "HERV_dup2159" "HERV_dup1383"
## [517] "HERV_dup894" "HERV_dup419" "HERV_dup1617" "HERV_dup2476"
## [521] "HERV_dup2182" "HERV_dup1447" "HERV_dup3459" "HERV_dup626"
## [525] "HERV_dup2041" "HERV_dup640" "HERV_dup1324" "HERV_dup934"
## [529] "HERV_dup3341" "HERV_dup2934" "HERV_dup329" "HERV_dup1780"
## [533] "HERV_dup3107" "HERV_dup1914" "HERV_dup1655" "HERV_dup1707"
## [537] "HERV_dup1319" "HERV_dup2379" "HERV_dup277" "HERV_dup2282"
## [541] "HERV_dup1868" "HERV_dup1470" "HERV_dup873" "HERV_dup975"
## [545] "HERV_dup2530" "HERV_dup2500" "HERV_dup112" "HERV_dup1307"
## [549] "HERV_dup632" "HERV_dup1303" "HERV_dup1935" "HERV_dup1614"
## [553] "HERV_dup2002" "HERV_dup1201" "HERV_dup1661" "HERV_dup488"
## [557] "HERV_dup1923" "HERV_dup597" "HERV_dup909" "HERV_dup3351"
## [561] "HERV_dup2891" "HERV_dup203" "HERV_dup1413" "HERV_dup1541"
## [565] "HERV_dup1080" "HERV_dup1316" "HERV_dup1401" "HERV_dup1719"
## [569] "HERV_dup2112" "HERV_dup933" "HERV_dup1240" "HERV_dup434"
## [573] "HERV_dup1750" "HERV_dup1449" "HERV_dup969" "HERV_dup65"
## [577] "HERV_dup2739" "HERV_dup3020" "HERV_dup2524" "HERV_dup54"
## [581] "HERV_dup671" "HERV_dup670" "HERV_dup777" "HERV_dup2298"
## [585] "HERV_dup703" "HERV_dup214" "HERV_dup249" "HERV_dup2012"
## [589] "HERV_dup2877" "HERV_dup2966" "HERV_dup2019" "HERV_dup2856"
## [593] "HERV_dup2598" "HERV_dup2299" "HERV_dup1888" "HERV_dup1255"
## [597] "HERV_dup1232" "HERV_dup1756" "HERV_dup1973" "HERV_dup1283"
## [601] "HERV_dup3388" "HERV_dup3417" "HERV_dup3390" "HERV_dup1102"
## [605] "HERV_dup2961" "HERV_dup1297" "HERV_dup1357" "HERV_dup1002"
## [609] "HERV_dup1484" "HERV_dup2914" "HERV_dup954" "HERV_dup1203"
## [613] "HERV_dup2085" "HERV_dup1694" "HERV_dup1004" "HERV_dup1308"
## [617] "HERV_dup1917" "HERV_dup482" "HERV_dup2438" "HERV_dup872"
## [621] "HERV_dup1317" "HERV_dup2803" "HERV_dup1671" "HERV_dup3365"
## [625] "HERV_dup3198" "HERV_dup2106" "HERV_dup1281" "HERV_dup3410"
## [629] "HERV_dup1209" "HERV_dup949" "HERV_dup3266" "HERV_dup2695"
## [633] "HERV_dup1702" "HERV_dup3418" "HERV_dup880" "HERV_dup1940"
## [637] "HERV_dup2261" "HERV_dup2623" "HERV_dup612" "HERV_dup290"
## [641] "HERV_dup470" "HERV_dup468" "HERV_dup939" "HERV_dup1982"
## [645] "HERV_dup3251" "HERV_dup2769" "HERV_dup2588" "HERV_dup93"
## [649] "HERV_dup2589" "HERV_dup1663" "HERV_dup1001" "HERV_dup1846"
## [653] "HERV_dup1847" "HERV_dup980" "HERV_dup2550" "HERV_dup1371"
## [657] "HERV_dup26" "HERV_dup94" "HERV_dup3220" "HERV_dup1235"
## [661] "HERV_dup1243" "HERV_dup3033" "HERV_dup2902" "HERV_dup990"
## [665] "HERV_dup956" "HERV_dup417" "HERV_dup913" "HERV_dup2812"
## [669] "HERV_dup2631" "HERV_dup36" "HERV_dup1512" "HERV_dup2915"
## [673] "HERV_dup3529" "HERV_dup3343" "HERV_dup3342" "HERV_dup1456"
## [677] "HERV_dup265" "HERV_dup1" "HERV_dup2789" "HERV_dup1382"
## [681] "HERV_dup2643" "HERV_dup2134" "HERV_dup61" "HERV_dup1358"
## [685] "HERV_dup302" "HERV_dup1889" "HERV_dup600" "HERV_dup717"
## [689] "HERV_dup927" "HERV_dup2412" "HERV_dup2376" "HERV_dup2896"
## [693] "HERV_dup2176" "HERV_dup1596" "HERV_dup2111" "HERV_dup1703"
## [697] "HERV_dup292" "HERV_dup1802" "HERV_dup1315" "L1PA2_dup39"
## [701] "L1PA3_dup9473" "L1PA2_dup3622" "L1PA3_dup3502" "L1HS_dup155"
## [705] "L1PA3_dup5418" "L1HS_dup831" "L1PA2_dup1621" "L1PA3_dup2683"
## [709] "L1PA2_dup2496" "L1PA3_dup4884" "L1PA3_dup4596" "L1PA2_dup4651"
## [713] "L1PA3_dup2662" "L1PA2_dup595" "L1PA3_dup6966" "L1PA3_dup6584"
## [717] "L1PA3_dup7792" "L1PA2_dup1746" "L1PA3_dup4668" "L1PA2_dup3405"
## [721] "L1PA2_dup678" "L1PA2_dup994" "L1PA2_dup2430" "L1PA3_dup7316"
## [725] "L1PA2_dup684" "L1PA3_dup5594" "L1PA3_dup1114" "L1PA3_dup6692"
## [729] "L1HS_dup244" "L1PA2_dup4378" "L1PA2_dup2261" "L1PA3_dup10525"
## [733] "L1HS_dup649" "L1HS_dup1576" "L1PA3_dup7947" "L1PA3_dup3404"
## [737] "L1PA3_dup1463" "L1HS_dup1473" "L1PA3_dup5825" "L1PA2_dup382"
## [741] "L1PA2_dup472" "L1PA2_dup2436" "L1PA2_dup3118" "L1HS_dup444"
## [745] "L1PA2_dup4612" "L1PA3_dup1943" "L1HS_dup1437" "L1PA3_dup9866"
## [749] "L1HS_dup370" "L1PA3_dup840" "L1HS_dup1501" "L1PA2_dup1177"
## [753] "L1PA3_dup5927" "L1HS_dup1616" "L1PA2_dup2004" "L1PA2_dup3439"
## [757] "L1PA2_dup4528" "L1PA2_dup2127" "L1PA2_dup4430" "L1PA2_dup109"
## [761] "L1PA2_dup1476" "L1HS_dup466" "L1PA3_dup5886" "L1PA3_dup1046"
## [765] "L1PA3_dup1727" "L1HS_dup376" "L1HS_dup204" "L1PA2_dup2444"
## [769] "L1PA2_dup4389" "L1PA2_dup4639" "L1PA2_dup3629" "L1PA2_dup726"
## [773] "L1HS_dup787" "L1PA2_dup3426" "L1PA2_dup732" "L1HS_dup225"
## [777] "L1HS_dup1014" "L1PA3_dup638" "L1PA2_dup3160" "L1HS_dup429"
## [781] "L1PA2_dup2504" "L1HS_dup802" "L1PA2_dup1049" "L1HS_dup1284"
## [785] "L1PA3_dup247" "L1PA3_dup9722" "L1PA3_dup3484" "L1HS_dup1342"
## [789] "L1PA3_dup10072" "L1PA3_dup9702" "L1PA2_dup3776" "L1PA2_dup1463"
## [793] "L1PA3_dup3959" "L1PA2_dup2537" "L1PA3_dup7288" "L1HS_dup90"
## [797] "L1PA3_dup6387" "L1PA2_dup2168" "L1PA3_dup7893" "L1PA2_dup759"
## [801] "L1PA2_dup3766" "L1PA3_dup3586" "L1PA2_dup1426" "L1PA2_dup4522"
## [805] "L1HS_dup1339" "L1PA2_dup589" "L1PA2_dup798" "L1PA2_dup2180"
## [809] "L1PA2_dup2876" "L1PA3_dup6523" "L1HS_dup600" "L1PA3_dup6871"
## [813] "L1PA2_dup1490" "L1PA2_dup1992" "L1PA2_dup4791" "L1PA3_dup8117"
## [817] "L1HS_dup1514" "L1PA2_dup4432" "L1PA2_dup4652" "L1PA2_dup2565"
## [821] "L1PA2_dup4196" "L1PA2_dup4478" "L1HS_dup87" "L1PA3_dup5866"
## [825] "L1PA2_dup4611" "L1PA3_dup1647" "L1PA2_dup935" "L1PA3_dup9202"
## [829] "L1PA3_dup8891" "L1PA3_dup4687" "L1PA3_dup5540" "L1PA2_dup1112"
## [833] "L1PA3_dup3291" "L1HS_dup111" "L1HS_dup163" "L1HS_dup1005"
## [837] "L1HS_dup1243" "L1PA2_dup4421" "L1PA2_dup4454" "L1PA3_dup2620"
## [841] "L1HS_dup1077" "L1PA2_dup4335" "L1PA3_dup1337" "L1HS_dup622"
## [845] "L1HS_dup1295" "L1PA2_dup219" "L1PA2_dup3445" "L1PA3_dup8506"
## [849] "L1HS_dup1393" "L1PA2_dup4936" "L1PA2_dup2577" "L1PA3_dup3684"
## [853] "L1PA3_dup10043" "L1HS_dup579" "L1PA2_dup2295" "L1PA3_dup1989"
## [857] "L1PA2_dup4237" "L1PA3_dup5057" "L1HS_dup811" "L1HS_dup1478"
## [861] "L1PA2_dup365" "L1PA2_dup4441" "L1PA2_dup358" "L1PA3_dup4349"
## [865] "L1PA2_dup4686" "L1PA2_dup307" "L1PA3_dup683" "L1PA3_dup1328"
## [869] "L1PA2_dup2047" "L1PA2_dup4548" "L1PA2_dup4262" "L1PA3_dup5363"
## [873] "L1HS_dup143" "L1PA2_dup4713" "L1PA3_dup4393" "L1PA3_dup3153"
## [877] "L1PA3_dup1528" "L1PA2_dup1653" "L1PA2_dup383" "L1PA2_dup1331"
## [881] "L1PA3_dup345" "L1PA2_dup1050" "L1PA2_dup2089" "L1PA2_dup1078"
## [885] "L1PA2_dup4201" "L1HS_dup1020" "L1PA2_dup1978" "L1PA3_dup10176"
## [889] "L1PA2_dup514" "L1PA3_dup8313" "L1PA2_dup629" "L1PA2_dup2506"
## [893] "L1PA2_dup4762" "L1PA3_dup10096" "L1PA2_dup3503" "L1PA3_dup5047"
## [897] "L1HS_dup35" "L1HS_dup62" "L1PA2_dup360" "L1PA2_dup4776"
## [901] "L1PA3_dup1279" "L1PA3_dup5106" "L1PA3_dup2755" "L1PA2_dup1248"
## [905] "L1HS_dup743" "L1PA2_dup3930" "L1PA2_dup4226" "L1PA3_dup5207"
## [909] "L1HS_dup679" "L1PA2_dup4688" "L1PA3_dup2389" "L1HS_dup1357"
## [913] "L1HS_dup803" "L1PA2_dup423" "L1PA3_dup3005" "L1PA2_dup747"
## [917] "L1PA2_dup1023" "L1PA3_dup5928" "L1PA2_dup2581" "L1PA2_dup2271"
## [921] "L1PA3_dup7432" "L1PA3_dup5544" "L1PA2_dup4901" "L1HS_dup1286"
## [925] "L1PA2_dup2729" "L1HS_dup1104" "L1PA3_dup1550" "L1PA3_dup9840"
## [929] "L1PA2_dup2282" "L1PA2_dup4309" "L1PA2_dup4618" "L1PA3_dup9255"
## [933] "L1PA2_dup326" "L1PA2_dup1058" "L1PA2_dup675" "L1PA3_dup5745"
## [937] "L1PA2_dup4074" "L1PA3_dup8173" "L1PA3_dup5468" "L1PA2_dup2254"
## [941] "L1PA2_dup3484" "L1PA2_dup727" "L1PA2_dup3579" "L1PA3_dup7840"
## [945] "L1PA3_dup1428" "L1HS_dup1182" "L1PA3_dup10344" "L1PA3_dup4408"
## [949] "L1PA3_dup6008" "L1PA2_dup3283" "L1HS_dup879" "L1PA2_dup4045"
## [953] "L1HS_dup907" "L1PA3_dup1027" "L1PA3_dup1026" "L1PA3_dup5358"
## [957] "L1PA3_dup5355" "L1PA3_dup3323" "L1PA3_dup1770" "L1PA2_dup805"
## [961] "L1PA2_dup949" "L1PA2_dup2408" "L1PA3_dup8896" "L1PA2_dup3773"
## [965] "L1PA3_dup3300" "L1PA3_dup3763" "L1PA2_dup3292" "L1PA3_dup8328"
## [969] "L1PA3_dup6160" "L1PA2_dup741" "L1PA3_dup9373" "L1HS_dup995"
## [973] "L1PA2_dup4053" "L1PA2_dup3003" "L1PA3_dup9734" "L1PA2_dup1560"
## [977] "L1PA2_dup4043" "L1PA3_dup10011" "L1PA3_dup6436" "L1HS_dup1324"
## [981] "L1PA3_dup10531" "L1PA2_dup1968" "L1PA2_dup98" "L1HS_dup1019"
## [985] "L1PA3_dup400" "L1PA3_dup2643" "L1PA3_dup3950" "L1PA3_dup7605"
## [989] "L1PA3_dup9856" "L1PA3_dup3880" "L1PA3_dup8310" "L1PA2_dup4030"
## [993] "L1PA2_dup1953" "L1PA2_dup4440" "L1PA2_dup2969" "L1PA2_dup1770"
## [997] "L1PA2_dup2155" "L1PA3_dup1269" "L1PA2_dup1805" "L1PA3_dup7550"
## [1001] "L1PA3_dup4708" "L1PA3_dup5534" "L1PA3_dup3968" "L1PA3_dup2393"
## [1005] "L1PA3_dup5238" "L1PA3_dup978" "L1PA3_dup4259" "L1PA3_dup1554"
## [1009] "L1PA2_dup2343" "L1PA2_dup413" "L1HS_dup270" "L1PA3_dup3954"
## [1013] "L1PA3_dup358" "L1PA2_dup1398" "L1PA3_dup1547" "L1PA2_dup2863"
## [1017] "L1PA3_dup6317" "L1PA2_dup1375" "L1PA3_dup8007" "L1PA3_dup2357"
## [1021] "L1PA3_dup165" "L1PA2_dup71" "L1PA2_dup142" "L1PA2_dup1933"
## [1025] "L1PA3_dup4688" "L1PA3_dup1264" "L1PA2_dup3607" "L1PA2_dup3881"
## [1029] "L1PA2_dup1778" "L1PA3_dup4709" "L1PA3_dup1800" "L1PA2_dup663"
## [1033] "L1HS_dup1536" "L1HS_dup632" "L1PA2_dup559" "L1PA3_dup4902"
## [1037] "L1PA2_dup2289" "L1PA2_dup526" "L1PA2_dup1418" "L1PA2_dup378"
## [1041] "L1PA3_dup398" "L1PA3_dup7237" "L1PA3_dup10285" "L1PA3_dup2557"
## [1045] "L1PA3_dup9095" "L1PA3_dup4994" "L1PA2_dup791" "L1PA3_dup10119"
## [1049] "L1PA3_dup8525" "L1PA3_dup2517" "L1PA3_dup1311" "L1PA3_dup6434"
## [1053] "L1PA2_dup922" "L1PA2_dup1230" "L1PA3_dup2593" "L1PA3_dup2919"
## [1057] "L1PA2_dup3664" "L1PA3_dup8663" "L1PA3_dup6573" "L1PA3_dup7470"
## [1061] "L1PA2_dup234" "L1PA3_dup2744" "L1PA2_dup37" "L1PA2_dup3136"
## [1065] "L1HS_dup800" "L1PA2_dup130" "L1PA3_dup3307" "L1PA2_dup3805"
## [1069] "L1PA3_dup3168" "L1PA3_dup7862" "L1PA2_dup4620" "L1HS_dup1462"
## [1073] "L1PA2_dup4403" "L1PA2_dup3771" "L1PA3_dup10297" "L1PA2_dup3589"
## [1077] "L1HS_dup1330" "L1PA2_dup1298" "L1PA2_dup2909" "L1PA2_dup3736"
## [1081] "L1PA3_dup4891" "L1PA3_dup4401" "L1PA3_dup5680" "L1PA3_dup7821"
## [1085] "L1PA2_dup1752" "L1PA3_dup10740" "L1PA3_dup1710" "L1PA3_dup4391"
## [1089] "L1PA3_dup5121" "L1PA3_dup5514" "L1PA3_dup3757" "L1PA3_dup3758"
## [1093] "L1PA2_dup1272" "L1PA3_dup1010" "L1PA3_dup4492" "L1PA2_dup2245"
## [1097] "L1PA2_dup927" "L1PA3_dup373" "L1PA3_dup1756" "L1PA3_dup529"
## [1101] "L1HS_dup455" "L1PA3_dup2760" "L1PA2_dup410" "L1HS_dup514"
## [1105] "L1PA2_dup2860" "L1PA2_dup2680" "L1PA2_dup1462" "L1PA3_dup2551"
## [1109] "L1PA3_dup9021" "L1PA2_dup2091" "L1PA3_dup6036" "L1PA2_dup4905"
## [1113] "L1PA3_dup5337" "L1PA3_dup9998" "L1PA3_dup6347" "L1PA2_dup3437"
## [1117] "L1PA2_dup3531" "L1PA3_dup6550" "L1PA2_dup530" "L1PA3_dup7864"
## [1121] "L1PA2_dup3615" "L1PA3_dup8872" "L1PA3_dup2721" "L1PA2_dup4838"
## [1125] "L1PA2_dup513" "L1PA2_dup3042" "L1PA2_dup737" "L1HS_dup596"
## [1129] "L1PA3_dup6730" "L1PA2_dup2385" "L1PA3_dup4603" "L1PA3_dup8520"
## [1133] "L1PA3_dup6929" "L1PA3_dup9946" "L1HS_dup124" "L1PA3_dup6884"
## [1137] "L1PA2_dup3425" "L1PA3_dup3729" "L1PA3_dup3863" "L1PA3_dup3102"
## [1141] "L1HS_dup449" "L1PA3_dup8420" "L1PA3_dup872" "L1PA3_dup2039"
## [1145] "L1PA2_dup4367" "L1PA2_dup635" "L1PA2_dup4775" "L1PA3_dup1952"
## [1149] "L1PA3_dup761" "L1PA3_dup6147" "L1PA3_dup3941" "L1PA3_dup4804"
## [1153] "L1PA2_dup2791" "L1PA3_dup907" "L1PA3_dup4885" "L1PA2_dup200"
## [1157] "L1PA2_dup1379" "L1HS_dup191" "L1PA3_dup7951" "L1PA3_dup6385"
## [1161] "L1PA3_dup2272" "L1PA3_dup7472" "L1PA3_dup7963" "L1PA2_dup221"
## [1165] "L1HS_dup788" "L1PA3_dup6002" "L1PA2_dup2164" "L1PA2_dup2988"
## [1169] "L1HS_dup379" "L1PA2_dup16" "L1HS_dup405" "L1PA2_dup3742"
## [1173] "L1PA3_dup3507" "L1PA3_dup9280" "L1HS_dup138" "L1HS_dup337"
## [1177] "L1PA3_dup4122" "L1PA3_dup2954" "L1PA2_dup1760" "L1PA2_dup4714"
## [1181] "L1PA3_dup1723" "L1PA3_dup124" "L1PA3_dup128" "L1PA3_dup8522"
## [1185] "L1PA3_dup3509" "L1PA3_dup1937" "L1PA3_dup6112" "L1PA2_dup4596"
## [1189] "L1PA3_dup4487" "L1HS_dup948" "L1PA3_dup3306" "L1PA3_dup8571"
## [1193] "L1PA2_dup1749" "L1PA3_dup9430" "L1HS_dup916" "L1PA3_dup561"
## [1197] "L1PA3_dup1988" "L1PA3_dup7637" "L1PA3_dup2204" "L1PA3_dup5510"
## [1201] "L1PA3_dup527" "L1PA2_dup662" "L1PA2_dup585" "L1PA2_dup2720"
## [1205] "L1PA3_dup748" "L1PA3_dup2413" "L1HS_dup240" "L1PA2_dup196"
## [1209] "L1PA3_dup1" "L1PA3_dup1651" "L1PA3_dup4118" "L1PA3_dup8903"
## [1213] "L1PA3_dup10686" "L1PA3_dup4888" "L1PA3_dup4277" "L1PA2_dup848"
## [1217] "L1PA3_dup6457" "L1PA3_dup9256"
asap_heatmap_snRNA(region = c("AMY"),
tes = data_TE_annotation$TE_id,
return_df = F, group_rows = c("type"), gaps_row = length(heatmap_amy_HERV_order),
breaks = seq(0,15,length.out = 52), index_row_reorder = c(heatmap_amy_HERV_order,heatmap_amy_L1_order),
order_cols_groups = order_cols_celltype,
data = TE_data, group_cols = c("celltype"),
title = "AMY HERVs + L1s: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
exclude_clusters = c(6, 7))

## $heatmap
##
## $order_cols
## [1] "DA805_ASAP56_ctrl_NP19-37_AMY_0" "AA_ASAP115_PD_NP21-208_AMY_0"
## [3] "DA474_ASAP24_PD_NP16-25_AMY_0" "AA_ASAP110_ctrl_NP16-119_AMY_0"
## [5] "DA811_ASAP18_PD_NP16-140_AMY_0" "DA778_ASAP31_PD_NP18-117_AMY_0"
## [7] "DA791_ASAP50_ctrl_NP18-159_AMY_0" "DA783_ASAP45_PD_NP19-255_AMY_0"
## [9] "DA793_ASAP53_ctrl_NP19-36_AMY_0" "DA780_ASAP37_PD_NP19-16_AMY_0"
## [11] "DA802_ASAP40_PD_NP19-23_AMY_0" "AA_ASAP114_PD_NP21-57_AMY_0"
## [13] "AA_ASAP123_ctrl_NP19-218_AMY_1" "AA_ASAP124_ctrl_NP22-37_AMY_1"
## [15] "AA_ASAP119_PD_NP22-55_AMY_1" "AA_ASAP114_PD_NP21-57_AMY_1"
## [17] "AA_ASAP113_ctrl_NP18-148_AMY_1" "AA_ASAP121_PD_NP17-232_AMY_1"
## [19] "AA_ASAP109_PD_NP21-217_AMY_1" "AA_ASAP128_PD_NP21-04_AMY_1"
## [21] "AA_ASAP131_PD_NP23-21_AMY_1" "AA_ASAP126_PD_NP19-137_AMY_1"
## [23] "DA811_ASAP18_PD_NP16-140_AMY_1" "DA802_ASAP40_PD_NP19-23_AMY_1"
## [25] "DA780_ASAP37_PD_NP19-16_AMY_1" "DA801_ASAP53_ctrl_NP19-36_AMY_1"
## [27] "DA805_ASAP56_ctrl_NP19-37_AMY_1" "DA474_ASAP24_PD_NP16-25_AMY_1"
## [29] "AA_ASAP115_PD_NP21-208_AMY_1" "AA_ASAP110_ctrl_NP16-119_AMY_1"
## [31] "DA512_ASAP60_ctrl_NP19-45_AMY_1" "DA778_ASAP31_PD_NP18-117_AMY_1"
## [33] "DA793_ASAP53_ctrl_NP19-36_AMY_1" "DA791_ASAP50_ctrl_NP18-159_AMY_1"
## [35] "DA783_ASAP45_PD_NP19-255_AMY_1" "ASAP122_PD_NP19-91_AMY_2"
## [37] "AA_ASAP109_PD_NP21-217_AMY_2" "AA_ASAP119_PD_NP22-55_AMY_2"
## [39] "AA_ASAP126_PD_NP19-137_AMY_2" "AA_ASAP131_PD_NP23-21_AMY_2"
## [41] "AA_ASAP128_PD_NP21-04_AMY_2" "DA807_ASAP29_PD_NP17-191_AMY_2"
## [43] "DA783_ASAP45_PD_NP19-255_AMY_2" "AA_ASAP115_PD_NP21-208_AMY_2"
## [45] "DA512_ASAP60_ctrl_NP19-45_AMY_2" "DA474_ASAP24_PD_NP16-25_AMY_2"
## [47] "AA_ASAP112_ctrl_NP16-293_AMY_2" "DA814_ASAP35_PD_NP18-304_AMY_2"
## [49] "AA_ASAP120_PD_NP16-285_AMY_2" "DA811_ASAP18_PD_NP16-140_AMY_2"
## [51] "AA_ASAP121_PD_NP17-232_AMY_2" "AA_ASAP124_ctrl_NP22-37_AMY_2"
## [53] "DA791_ASAP50_ctrl_NP18-159_AMY_2" "DA780_ASAP37_PD_NP19-16_AMY_2"
## [55] "DA802_ASAP40_PD_NP19-23_AMY_2" "AA_ASAP123_ctrl_NP19-218_AMY_2"
## [57] "DA805_ASAP56_ctrl_NP19-37_AMY_2" "DA793_ASAP53_ctrl_NP19-36_AMY_2"
## [59] "DA801_ASAP53_ctrl_NP19-36_AMY_2" "DA778_ASAP31_PD_NP18-117_AMY_2"
## [61] "AA_ASAP113_ctrl_NP18-148_AMY_2" "AA_ASAP110_ctrl_NP16-119_AMY_2"
## [63] "AA_ASAP114_PD_NP21-57_AMY_2" "DA783_ASAP45_PD_NP19-255_AMY_3"
## [65] "AA_ASAP121_PD_NP17-232_AMY_3" "AA_ASAP109_PD_NP21-217_AMY_3"
## [67] "DA802_ASAP40_PD_NP19-23_AMY_3" "ASAP122_PD_NP19-91_AMY_3"
## [69] "AA_ASAP120_PD_NP16-285_AMY_3" "AA_ASAP112_ctrl_NP16-293_AMY_3"
## [71] "AA_ASAP115_PD_NP21-208_AMY_3" "AA_ASAP131_PD_NP23-21_AMY_3"
## [73] "DA803_ASAP48_ctrl_NP17-256_AMY_3" "AA_ASAP111_ctrl_NP16-284_AMY_3"
## [75] "AA_ASAP124_ctrl_NP22-37_AMY_3" "AA_ASAP119_PD_NP22-55_AMY_3"
## [77] "DA807_ASAP29_PD_NP17-191_AMY_3" "DA811_ASAP18_PD_NP16-140_AMY_3"
## [79] "DA805_ASAP56_ctrl_NP19-37_AMY_3" "AA_ASAP110_ctrl_NP16-119_AMY_3"
## [81] "DA474_ASAP24_PD_NP16-25_AMY_3" "DA801_ASAP53_ctrl_NP19-36_AMY_3"
## [83] "DA793_ASAP53_ctrl_NP19-36_AMY_3" "DA778_ASAP31_PD_NP18-117_AMY_3"
## [85] "DA780_ASAP37_PD_NP19-16_AMY_3" "DA791_ASAP50_ctrl_NP18-159_AMY_3"
## [87] "AA_ASAP113_ctrl_NP18-148_AMY_3" "DA512_ASAP60_ctrl_NP19-45_AMY_3"
## [89] "AA_ASAP114_PD_NP21-57_AMY_3" "AA_ASAP123_ctrl_NP19-218_AMY_3"
## [91] "AA_ASAP128_PD_NP21-04_AMY_3" "DA512_ASAP60_ctrl_NP19-45_AMY_5"
## [93] "AA_ASAP126_PD_NP19-137_AMY_5" "AA_ASAP115_PD_NP21-208_AMY_5"
## [95] "AA_ASAP110_ctrl_NP16-119_AMY_5" "DA783_ASAP45_PD_NP19-255_AMY_5"
## [97] "DA802_ASAP40_PD_NP19-23_AMY_5" "DA778_ASAP31_PD_NP18-117_AMY_5"
## [99] "AA_ASAP131_PD_NP23-21_AMY_5" "AA_ASAP121_PD_NP17-232_AMY_5"
## [101] "DA800_ASAP20_PD_NP16-160_AMY_5" "AA_ASAP128_PD_NP21-04_AMY_5"
## [103] "AA_ASAP120_PD_NP16-285_AMY_5" "DA803_ASAP48_ctrl_NP17-256_AMY_5"
## [105] "ASAP122_PD_NP19-91_AMY_5" "AA_ASAP109_PD_NP21-217_AMY_5"
## [107] "DA474_ASAP24_PD_NP16-25_AMY_5" "DA805_ASAP56_ctrl_NP19-37_AMY_5"
## [109] "AA_ASAP113_ctrl_NP18-148_AMY_5" "AA_ASAP114_PD_NP21-57_AMY_5"
## [111] "DA791_ASAP50_ctrl_NP18-159_AMY_5" "AA_ASAP124_ctrl_NP22-37_AMY_5"
## [113] "AA_ASAP112_ctrl_NP16-293_AMY_5" "AA_ASAP119_PD_NP22-55_AMY_5"
## [115] "DA807_ASAP29_PD_NP17-191_AMY_5" "DA780_ASAP37_PD_NP19-16_AMY_5"
## [117] "DA801_ASAP53_ctrl_NP19-36_AMY_5" "DA793_ASAP53_ctrl_NP19-36_AMY_5"
## [119] "AA_ASAP123_ctrl_NP19-218_AMY_5" "DA811_ASAP18_PD_NP16-140_AMY_5"
## [121] "DA814_ASAP35_PD_NP18-304_AMY_5" "DA815_ASAP37_PD_NP19-16_AMY_5"
## [123] "DA779_ASAP33_PD_NP18-287_AMY_5" "DA802_ASAP40_PD_NP19-23_AMY_4"
## [125] "DA783_ASAP45_PD_NP19-255_AMY_4" "AA_ASAP131_PD_NP23-21_AMY_4"
## [127] "AA_ASAP112_ctrl_NP16-293_AMY_4" "AA_ASAP115_PD_NP21-208_AMY_4"
## [129] "DA512_ASAP60_ctrl_NP19-45_AMY_4" "AA_ASAP126_PD_NP19-137_AMY_4"
## [131] "DA811_ASAP18_PD_NP16-140_AMY_4" "DA791_ASAP50_ctrl_NP18-159_AMY_4"
## [133] "DA778_ASAP31_PD_NP18-117_AMY_4" "DA807_ASAP29_PD_NP17-191_AMY_4"
## [135] "DA801_ASAP53_ctrl_NP19-36_AMY_4" "DA805_ASAP56_ctrl_NP19-37_AMY_4"
## [137] "DA474_ASAP24_PD_NP16-25_AMY_4" "AA_ASAP119_PD_NP22-55_AMY_4"
## [139] "AA_ASAP123_ctrl_NP19-218_AMY_4" "AA_ASAP114_PD_NP21-57_AMY_4"
## [141] "AA_ASAP113_ctrl_NP18-148_AMY_4" "DA793_ASAP53_ctrl_NP19-36_AMY_4"
## [143] "AA_ASAP110_ctrl_NP16-119_AMY_4"
##
## $order_rows
## [1] "HERV_dup3118" "HERV_dup65" "HERV_dup670" "HERV_dup2524"
## [5] "HERV_dup671" "HERV_dup1417" "HERV_dup417" "HERV_dup2273"
## [9] "HERV_dup3143" "HERV_dup1613" "HERV_dup1195" "HERV_dup350"
## [13] "HERV_dup1416" "HERV_dup2353" "HERV_dup2422" "HERV_dup1875"
## [17] "HERV_dup2106" "HERV_dup214" "HERV_dup1281" "HERV_dup1209"
## [21] "HERV_dup2012" "HERV_dup2856" "HERV_dup2966" "HERV_dup2019"
## [25] "HERV_dup249" "HERV_dup2877" "HERV_dup36" "HERV_dup1917"
## [29] "HERV_dup3198" "HERV_dup380" "HERV_dup3355" "HERV_dup3505"
## [33] "HERV_dup3507" "HERV_dup1555" "HERV_dup2378" "HERV_dup2320"
## [37] "HERV_dup2188" "HERV_dup2743" "HERV_dup1272" "HERV_dup1556"
## [41] "HERV_dup2555" "HERV_dup492" "HERV_dup3335" "HERV_dup215"
## [45] "HERV_dup831" "HERV_dup3363" "HERV_dup1948" "HERV_dup1520"
## [49] "HERV_dup3171" "HERV_dup2646" "HERV_dup434" "HERV_dup1658"
## [53] "HERV_dup399" "HERV_dup2809" "HERV_dup2183" "HERV_dup723"
## [57] "HERV_dup1253" "HERV_dup3217" "HERV_dup2977" "HERV_dup3286"
## [61] "HERV_dup1730" "HERV_dup2696" "HERV_dup551" "HERV_dup3227"
## [65] "HERV_dup2728" "HERV_dup23" "HERV_dup369" "HERV_dup2879"
## [69] "HERV_dup1598" "HERV_dup2739" "HERV_dup2163" "HERV_dup1437"
## [73] "HERV_dup2607" "HERV_dup3351" "HERV_dup1345" "HERV_dup1114"
## [77] "HERV_dup1351" "HERV_dup2250" "HERV_dup1750" "HERV_dup2848"
## [81] "HERV_dup38" "HERV_dup1868" "HERV_dup2002" "HERV_dup2533"
## [85] "HERV_dup904" "HERV_dup1890" "HERV_dup377" "HERV_dup2733"
## [89] "HERV_dup1243" "HERV_dup2379" "HERV_dup1655" "HERV_dup3459"
## [93] "HERV_dup3328" "HERV_dup873" "HERV_dup2566" "HERV_dup3140"
## [97] "HERV_dup640" "HERV_dup2041" "HERV_dup2897" "HERV_dup3117"
## [101] "HERV_dup3341" "HERV_dup2934" "HERV_dup626" "HERV_dup1447"
## [105] "HERV_dup1080" "HERV_dup2476" "HERV_dup3231" "HERV_dup2769"
## [109] "HERV_dup1413" "HERV_dup329" "HERV_dup2112" "HERV_dup934"
## [113] "HERV_dup3107" "HERV_dup1703" "HERV_dup1282" "HERV_dup1617"
## [117] "HERV_dup3251" "HERV_dup1596" "HERV_dup1333" "HERV_dup1719"
## [121] "HERV_dup2651" "HERV_dup2985" "HERV_dup2962" "HERV_dup1048"
## [125] "HERV_dup300" "HERV_dup3124" "HERV_dup2438" "HERV_dup482"
## [129] "HERV_dup94" "HERV_dup1371" "HERV_dup1001" "HERV_dup26"
## [133] "HERV_dup980" "HERV_dup1846" "HERV_dup1847" "HERV_dup2550"
## [137] "HERV_dup293" "HERV_dup597" "HERV_dup799" "HERV_dup3148"
## [141] "HERV_dup909" "HERV_dup2179" "HERV_dup1953" "HERV_dup2500"
## [145] "HERV_dup3287" "HERV_dup990" "HERV_dup1663" "HERV_dup2855"
## [149] "HERV_dup1512" "HERV_dup1334" "HERV_dup899" "HERV_dup2235"
## [153] "HERV_dup1731" "HERV_dup1569" "HERV_dup2319" "HERV_dup2964"
## [157] "HERV_dup2282" "HERV_dup900" "HERV_dup773" "HERV_dup3105"
## [161] "HERV_dup1235" "HERV_dup2562" "HERV_dup2561" "HERV_dup1236"
## [165] "HERV_dup890" "HERV_dup54" "HERV_dup2963" "HERV_dup3220"
## [169] "HERV_dup151" "HERV_dup956" "HERV_dup1362" "HERV_dup2404"
## [173] "HERV_dup1657" "HERV_dup1321" "HERV_dup1319" "HERV_dup202"
## [177] "HERV_dup282" "HERV_dup218" "HERV_dup2366" "HERV_dup2784"
## [181] "HERV_dup2292" "HERV_dup2847" "HERV_dup2941" "HERV_dup446"
## [185] "HERV_dup2383" "HERV_dup2942" "HERV_dup441" "HERV_dup916"
## [189] "HERV_dup572" "HERV_dup1201" "HERV_dup1926" "HERV_dup1532"
## [193] "HERV_dup968" "HERV_dup1605" "HERV_dup1071" "HERV_dup1972"
## [197] "HERV_dup1156" "HERV_dup3694" "HERV_dup1780" "HERV_dup1304"
## [201] "HERV_dup1316" "HERV_dup2436" "HERV_dup1324" "HERV_dup203"
## [205] "HERV_dup2278" "HERV_dup2356" "HERV_dup3416" "HERV_dup58"
## [209] "HERV_dup108" "HERV_dup2785" "HERV_dup3239" "HERV_dup1541"
## [213] "HERV_dup710" "HERV_dup185" "HERV_dup3270" "HERV_dup591"
## [217] "HERV_dup433" "HERV_dup127" "HERV_dup803" "HERV_dup3406"
## [221] "HERV_dup39" "HERV_dup2290" "HERV_dup400" "HERV_dup1248"
## [225] "HERV_dup1089" "HERV_dup935" "HERV_dup57" "HERV_dup398"
## [229] "HERV_dup746" "HERV_dup133" "HERV_dup1187" "HERV_dup1210"
## [233] "HERV_dup1673" "HERV_dup1513" "HERV_dup2187" "HERV_dup3108"
## [237] "HERV_dup381" "HERV_dup568" "HERV_dup129" "HERV_dup728"
## [241] "HERV_dup1378" "HERV_dup1295" "HERV_dup84" "HERV_dup1638"
## [245] "HERV_dup177" "HERV_dup1869" "HERV_dup3481" "HERV_dup2482"
## [249] "HERV_dup1384" "HERV_dup2557" "HERV_dup1112" "HERV_dup1496"
## [253] "HERV_dup3073" "HERV_dup3137" "HERV_dup1239" "HERV_dup1639"
## [257] "HERV_dup2602" "HERV_dup1038" "HERV_dup2464" "HERV_dup180"
## [261] "HERV_dup1958" "HERV_dup1213" "HERV_dup2324" "HERV_dup2192"
## [265] "HERV_dup2518" "HERV_dup2129" "HERV_dup519" "HERV_dup1934"
## [269] "HERV_dup1374" "HERV_dup2945" "HERV_dup966" "HERV_dup321"
## [273] "HERV_dup3131" "HERV_dup357" "HERV_dup1724" "HERV_dup556"
## [277] "HERV_dup291" "HERV_dup2894" "HERV_dup1668" "HERV_dup184"
## [281] "HERV_dup2875" "HERV_dup3015" "HERV_dup1757" "HERV_dup967"
## [285] "HERV_dup1212" "HERV_dup930" "HERV_dup1937" "HERV_dup2655"
## [289] "HERV_dup3688" "HERV_dup3044" "HERV_dup469" "HERV_dup419"
## [293] "HERV_dup1403" "HERV_dup1331" "HERV_dup1500" "HERV_dup2034"
## [297] "HERV_dup3063" "HERV_dup1587" "HERV_dup389" "HERV_dup736"
## [301] "HERV_dup2972" "HERV_dup3154" "HERV_dup3182" "HERV_dup34"
## [305] "HERV_dup2949" "HERV_dup505" "HERV_dup1146" "HERV_dup924"
## [309] "HERV_dup595" "HERV_dup732" "HERV_dup729" "HERV_dup850"
## [313] "HERV_dup1415" "HERV_dup530" "HERV_dup1933" "HERV_dup1131"
## [317] "HERV_dup1629" "HERV_dup1278" "HERV_dup2337" "HERV_dup2479"
## [321] "HERV_dup452" "HERV_dup86" "HERV_dup2886" "HERV_dup2939"
## [325] "HERV_dup3008" "HERV_dup1003" "HERV_dup1733" "HERV_dup2878"
## [329] "HERV_dup517" "HERV_dup1005" "HERV_dup194" "HERV_dup3219"
## [333] "HERV_dup3588" "HERV_dup3037" "HERV_dup443" "HERV_dup1302"
## [337] "HERV_dup388" "HERV_dup2647" "HERV_dup29" "HERV_dup2747"
## [341] "HERV_dup634" "HERV_dup554" "HERV_dup201" "HERV_dup3016"
## [345] "HERV_dup1438" "HERV_dup2843" "HERV_dup2303" "HERV_dup355"
## [349] "HERV_dup1920" "HERV_dup1366" "HERV_dup894" "HERV_dup2967"
## [353] "HERV_dup115" "HERV_dup272" "HERV_dup467" "HERV_dup1007"
## [357] "HERV_dup1108" "HERV_dup2706" "HERV_dup682" "HERV_dup2620"
## [361] "HERV_dup450" "HERV_dup2603" "HERV_dup1514" "HERV_dup2272"
## [365] "HERV_dup2441" "HERV_dup3606" "HERV_dup1073" "HERV_dup1228"
## [369] "HERV_dup183" "HERV_dup2857" "HERV_dup1245" "HERV_dup471"
## [373] "HERV_dup2548" "HERV_dup1389" "HERV_dup1412" "HERV_dup3519"
## [377] "HERV_dup1327" "HERV_dup3210" "HERV_dup1653" "HERV_dup2907"
## [381] "HERV_dup2264" "HERV_dup2033" "HERV_dup2804" "HERV_dup692"
## [385] "HERV_dup1279" "HERV_dup1017" "HERV_dup2100" "HERV_dup1640"
## [389] "HERV_dup3673" "HERV_dup17" "HERV_dup1656" "HERV_dup1979"
## [393] "HERV_dup344" "HERV_dup870" "HERV_dup2529" "HERV_dup1390"
## [397] "HERV_dup1222" "HERV_dup2937" "HERV_dup2536" "HERV_dup356"
## [401] "HERV_dup1470" "HERV_dup331" "HERV_dup662" "HERV_dup1891"
## [405] "HERV_dup1720" "HERV_dup2891" "HERV_dup1047" "HERV_dup3394"
## [409] "HERV_dup120" "HERV_dup301" "HERV_dup724" "HERV_dup2152"
## [413] "HERV_dup2635" "HERV_dup3366" "HERV_dup599" "HERV_dup1052"
## [417] "HERV_dup2599" "HERV_dup1298" "HERV_dup1804" "HERV_dup975"
## [421] "HERV_dup1943" "HERV_dup1611" "HERV_dup243" "HERV_dup1356"
## [425] "HERV_dup2391" "HERV_dup776" "HERV_dup407" "HERV_dup1268"
## [429] "HERV_dup152" "HERV_dup613" "HERV_dup2604" "HERV_dup118"
## [433] "HERV_dup3179" "HERV_dup2149" "HERV_dup1090" "HERV_dup846"
## [437] "HERV_dup573" "HERV_dup933" "HERV_dup1029" "HERV_dup1242"
## [441] "HERV_dup3181" "HERV_dup2631" "HERV_dup1433" "HERV_dup3580"
## [445] "HERV_dup1381" "HERV_dup852" "HERV_dup18" "HERV_dup3430"
## [449] "HERV_dup2663" "HERV_dup2653" "HERV_dup3013" "HERV_dup1778"
## [453] "HERV_dup3031" "HERV_dup3050" "HERV_dup1962" "HERV_dup977"
## [457] "HERV_dup882" "HERV_dup2130" "HERV_dup565" "HERV_dup2480"
## [461] "HERV_dup348" "HERV_dup1453" "HERV_dup336" "HERV_dup251"
## [465] "HERV_dup508" "HERV_dup631" "HERV_dup2632" "HERV_dup1346"
## [469] "HERV_dup1107" "HERV_dup1526" "HERV_dup5" "HERV_dup1752"
## [473] "HERV_dup250" "HERV_dup1208" "HERV_dup3100" "HERV_dup1184"
## [477] "HERV_dup1661" "HERV_dup487" "HERV_dup2159" "HERV_dup1755"
## [481] "HERV_dup981" "HERV_dup577" "HERV_dup1099" "HERV_dup2840"
## [485] "HERV_dup1491" "HERV_dup21" "HERV_dup1273" "HERV_dup586"
## [489] "HERV_dup982" "HERV_dup735" "HERV_dup1103" "HERV_dup2936"
## [493] "HERV_dup665" "HERV_dup1851" "HERV_dup3284" "HERV_dup1049"
## [497] "HERV_dup1218" "HERV_dup1093" "HERV_dup570" "HERV_dup2823"
## [501] "HERV_dup3212" "HERV_dup1902" "HERV_dup3215" "HERV_dup2242"
## [505] "HERV_dup1579" "HERV_dup3187" "HERV_dup2415" "HERV_dup2730"
## [509] "HERV_dup1036" "HERV_dup3196" "HERV_dup1932" "HERV_dup2978"
## [513] "HERV_dup2979" "HERV_dup3189" "HERV_dup1823" "HERV_dup1459"
## [517] "HERV_dup1350" "HERV_dup1064" "HERV_dup1046" "HERV_dup876"
## [521] "HERV_dup2735" "HERV_dup1440" "HERV_dup578" "HERV_dup1383"
## [525] "HERV_dup1303" "HERV_dup1935" "HERV_dup2128" "HERV_dup2680"
## [529] "HERV_dup3319" "HERV_dup1557" "HERV_dup2778" "HERV_dup110"
## [533] "HERV_dup2530" "HERV_dup277" "HERV_dup1401" "HERV_dup1364"
## [537] "HERV_dup2797" "HERV_dup1707" "HERV_dup1914" "HERV_dup1082"
## [541] "HERV_dup1081" "HERV_dup409" "HERV_dup2736" "HERV_dup3358"
## [545] "HERV_dup2905" "HERV_dup1269" "HERV_dup488" "HERV_dup27"
## [549] "HERV_dup2801" "HERV_dup703" "HERV_dup851" "HERV_dup2334"
## [553] "HERV_dup2166" "HERV_dup1050" "HERV_dup2900" "HERV_dup386"
## [557] "HERV_dup1717" "HERV_dup1285" "HERV_dup632" "HERV_dup1339"
## [561] "HERV_dup1240" "HERV_dup112" "HERV_dup2182" "HERV_dup2027"
## [565] "HERV_dup3522" "HERV_dup2772" "HERV_dup276" "HERV_dup1614"
## [569] "HERV_dup1322" "HERV_dup2525" "HERV_dup2834" "HERV_dup758"
## [573] "HERV_dup1307" "HERV_dup1662" "HERV_dup1923" "HERV_dup1359"
## [577] "HERV_dup2093" "HERV_dup2365" "HERV_dup562" "HERV_dup777"
## [581] "HERV_dup1394" "HERV_dup2298" "HERV_dup2376" "HERV_dup2896"
## [585] "HERV_dup93" "HERV_dup2588" "HERV_dup2589" "HERV_dup2176"
## [589] "HERV_dup1802" "HERV_dup2111" "HERV_dup880" "HERV_dup3365"
## [593] "HERV_dup1940" "HERV_dup2643" "HERV_dup292" "HERV_dup1456"
## [597] "HERV_dup2598" "HERV_dup1315" "HERV_dup290" "HERV_dup1317"
## [601] "HERV_dup2623" "HERV_dup2803" "HERV_dup1671" "HERV_dup1232"
## [605] "HERV_dup1888" "HERV_dup2261" "HERV_dup1382" "HERV_dup872"
## [609] "HERV_dup1973" "HERV_dup1102" "HERV_dup1357" "HERV_dup3390"
## [613] "HERV_dup954" "HERV_dup1297" "HERV_dup1484" "HERV_dup2914"
## [617] "HERV_dup3266" "HERV_dup2085" "HERV_dup3410" "HERV_dup1694"
## [621] "HERV_dup1004" "HERV_dup949" "HERV_dup1203" "HERV_dup939"
## [625] "HERV_dup470" "HERV_dup468" "HERV_dup2915" "HERV_dup612"
## [629] "HERV_dup474" "HERV_dup2902" "HERV_dup1982" "HERV_dup2299"
## [633] "HERV_dup2695" "HERV_dup1702" "HERV_dup3418" "HERV_dup3529"
## [637] "HERV_dup518" "HERV_dup3379" "HERV_dup3226" "HERV_dup1310"
## [641] "HERV_dup2752" "HERV_dup2158" "HERV_dup1756" "HERV_dup302"
## [645] "HERV_dup1889" "HERV_dup1283" "HERV_dup717" "HERV_dup600"
## [649] "HERV_dup2412" "HERV_dup2961" "HERV_dup1002" "HERV_dup927"
## [653] "HERV_dup1670" "HERV_dup1308" "HERV_dup3388" "HERV_dup3417"
## [657] "HERV_dup384" "HERV_dup2266" "HERV_dup1309" "HERV_dup37"
## [661] "HERV_dup61" "HERV_dup3174" "HERV_dup3423" "HERV_dup2491"
## [665] "HERV_dup3343" "HERV_dup3342" "HERV_dup2789" "HERV_dup1"
## [669] "HERV_dup265" "HERV_dup1358" "HERV_dup2134" "HERV_dup940"
## [673] "HERV_dup3252" "HERV_dup614" "HERV_dup2662" "HERV_dup2841"
## [677] "HERV_dup288" "HERV_dup1000" "HERV_dup1669" "HERV_dup1701"
## [681] "HERV_dup731" "HERV_dup3375" "HERV_dup379" "HERV_dup3357"
## [685] "HERV_dup2838" "HERV_dup1758" "HERV_dup1079" "HERV_dup1708"
## [689] "HERV_dup2880" "HERV_dup2381" "HERV_dup1255" "HERV_dup926"
## [693] "HERV_dup913" "HERV_dup1749" "HERV_dup2812" "HERV_dup3033"
## [697] "HERV_dup979" "HERV_dup3020" "HERV_dup1449" "HERV_dup969"
## [701] "HERV_dup209" "L1PA3_dup3763" "L1HS_dup62" "L1PA2_dup1375"
## [705] "L1PA3_dup7432" "L1PA2_dup1621" "L1PA2_dup4043" "L1PA3_dup8313"
## [709] "L1PA2_dup3622" "L1PA2_dup2496" "L1PA2_dup4309" "L1HS_dup405"
## [713] "L1PA2_dup1746" "L1PA2_dup39" "L1PA3_dup1723" "L1PA3_dup4884"
## [717] "L1PA2_dup4651" "L1PA3_dup3509" "L1PA2_dup2343" "L1PA3_dup1554"
## [721] "L1PA2_dup4226" "L1PA3_dup2683" "L1PA3_dup6160" "L1PA2_dup595"
## [725] "L1PA2_dup678" "L1PA2_dup326" "L1PA3_dup10176" "L1PA3_dup2954"
## [729] "L1PA3_dup4596" "L1PA2_dup3003" "L1HS_dup916" "L1PA2_dup4053"
## [733] "L1PA3_dup8328" "L1PA2_dup741" "L1PA3_dup9373" "L1PA3_dup6584"
## [737] "L1PA3_dup3502" "L1PA3_dup10344" "L1PA3_dup7792" "L1PA2_dup16"
## [741] "L1PA2_dup1560" "L1PA3_dup4668" "L1PA3_dup5418" "L1PA2_dup2581"
## [745] "L1HS_dup155" "L1PA3_dup7864" "L1PA2_dup3615" "L1PA2_dup2155"
## [749] "L1PA2_dup4714" "L1PA2_dup2969" "L1PA3_dup8522" "L1PA2_dup4440"
## [753] "L1PA2_dup1749" "L1PA3_dup1988" "L1PA2_dup4596" "L1PA3_dup4487"
## [757] "L1PA2_dup4775" "L1PA3_dup1952" "L1HS_dup379" "L1PA2_dup3742"
## [761] "L1HS_dup948" "L1PA3_dup1937" "L1PA3_dup6112" "L1PA3_dup3306"
## [765] "L1PA3_dup7316" "L1PA2_dup4905" "L1PA2_dup1653" "L1PA3_dup1027"
## [769] "L1PA3_dup6929" "L1PA3_dup9998" "L1PA3_dup5745" "L1PA3_dup3307"
## [773] "L1PA2_dup3042" "L1PA3_dup6347" "L1PA3_dup5468" "L1PA2_dup3579"
## [777] "L1PA2_dup2254" "L1PA3_dup1550" "L1PA2_dup727" "L1PA2_dup3484"
## [781] "L1PA2_dup675" "L1PA2_dup4074" "L1PA3_dup7840" "L1PA3_dup8173"
## [785] "L1PA3_dup9946" "L1PA3_dup3323" "L1PA3_dup3300" "L1PA3_dup8420"
## [789] "L1PA3_dup1428" "L1PA3_dup1463" "L1PA3_dup3950" "L1PA2_dup4936"
## [793] "L1PA3_dup4408" "L1PA3_dup3880" "L1PA2_dup1331" "L1PA2_dup949"
## [797] "L1PA2_dup1078" "L1HS_dup1104" "L1HS_dup907" "L1HS_dup1324"
## [801] "L1PA2_dup684" "L1PA2_dup2577" "L1PA3_dup1528" "L1PA3_dup8896"
## [805] "L1PA2_dup4045" "L1PA3_dup5358" "L1PA3_dup5355" "L1PA3_dup6884"
## [809] "L1PA3_dup1770" "L1HS_dup124" "L1PA2_dup805" "L1PA2_dup3773"
## [813] "L1PA3_dup400" "L1PA3_dup10072" "L1PA3_dup1026" "L1PA3_dup3484"
## [817] "L1PA3_dup4393" "L1PA3_dup9722" "L1HS_dup879" "L1PA3_dup2643"
## [821] "L1PA3_dup9856" "L1PA3_dup6008" "L1PA3_dup3729" "L1PA2_dup3425"
## [825] "L1PA3_dup3954" "L1PA3_dup1547" "L1PA2_dup413" "L1PA3_dup10525"
## [829] "L1PA3_dup6317" "L1PA3_dup9255" "L1PA3_dup9840" "L1PA2_dup2863"
## [833] "L1PA3_dup10096" "L1PA2_dup1770" "L1PA2_dup994" "L1PA2_dup2430"
## [837] "L1PA3_dup5047" "L1HS_dup831" "L1PA2_dup3503" "L1PA2_dup219"
## [841] "L1PA2_dup4688" "L1PA2_dup747" "L1PA3_dup5106" "L1PA2_dup514"
## [845] "L1HS_dup1005" "L1HS_dup995" "L1PA2_dup383" "L1PA2_dup1112"
## [849] "L1PA3_dup4259" "L1PA3_dup5866" "L1PA3_dup2755" "L1HS_dup270"
## [853] "L1PA3_dup1279" "L1PA3_dup3005" "L1PA2_dup4454" "L1HS_dup225"
## [857] "L1HS_dup649" "L1HS_dup811" "L1PA3_dup6387" "L1PA3_dup8506"
## [861] "L1PA2_dup4762" "L1PA3_dup7947" "L1PA2_dup2089" "L1PA2_dup2729"
## [865] "L1HS_dup579" "L1HS_dup1295" "L1HS_dup1020" "L1PA2_dup3445"
## [869] "L1PA3_dup5928" "L1PA3_dup5927" "L1PA2_dup4686" "L1PA3_dup1989"
## [873] "L1PA2_dup3776" "L1PA3_dup6692" "L1PA2_dup2282" "L1PA2_dup2295"
## [877] "L1PA2_dup629" "L1HS_dup787" "L1PA2_dup360" "L1PA2_dup358"
## [881] "L1PA2_dup2168" "L1PA2_dup2506" "L1PA3_dup1328" "L1HS_dup622"
## [885] "L1PA2_dup1426" "L1PA3_dup345" "L1PA3_dup10043" "L1PA2_dup4522"
## [889] "L1PA2_dup4639" "L1HS_dup370" "L1PA2_dup4611" "L1HS_dup1393"
## [893] "L1PA2_dup4201" "L1PA3_dup7893" "L1HS_dup1243" "L1PA3_dup5594"
## [897] "L1HS_dup90" "L1PA2_dup2565" "L1PA2_dup759" "L1PA2_dup726"
## [901] "L1PA3_dup247" "L1HS_dup244" "L1HS_dup1514" "L1PA2_dup1463"
## [905] "L1HS_dup1077" "L1PA3_dup2389" "L1HS_dup679" "L1PA3_dup638"
## [909] "L1PA2_dup4548" "L1HS_dup466" "L1PA2_dup1476" "L1PA2_dup2047"
## [913] "L1HS_dup111" "L1PA2_dup4378" "L1PA2_dup2180" "L1PA3_dup10531"
## [917] "L1PA3_dup1046" "L1PA3_dup8117" "L1PA3_dup3404" "L1PA3_dup9202"
## [921] "L1HS_dup1342" "L1PA2_dup2004" "L1PA2_dup1177" "L1PA3_dup6871"
## [925] "L1PA2_dup4612" "L1PA2_dup4430" "L1HS_dup163" "L1PA2_dup1992"
## [929] "L1PA3_dup5363" "L1PA3_dup3153" "L1HS_dup1339" "L1PA2_dup3439"
## [933] "L1PA2_dup4196" "L1PA3_dup5886" "L1PA2_dup935" "L1PA2_dup4713"
## [937] "L1PA2_dup1398" "L1PA2_dup1490" "L1PA3_dup3684" "L1PA2_dup3160"
## [941] "L1PA2_dup109" "L1PA2_dup307" "L1PA3_dup1647" "L1PA2_dup732"
## [945] "L1PA2_dup2436" "L1PA3_dup5540" "L1PA2_dup3426" "L1PA3_dup840"
## [949] "L1PA3_dup9866" "L1PA3_dup1727" "L1HS_dup802" "L1PA3_dup683"
## [953] "L1HS_dup429" "L1PA2_dup4791" "L1PA2_dup4652" "L1HS_dup1616"
## [957] "L1HS_dup204" "L1PA3_dup5825" "L1HS_dup87" "L1PA2_dup2504"
## [961] "L1PA2_dup4528" "L1PA2_dup4432" "L1PA3_dup3959" "L1HS_dup1473"
## [965] "L1HS_dup444" "L1PA3_dup6523" "L1PA2_dup798" "L1HS_dup143"
## [969] "L1PA3_dup3586" "L1PA2_dup589" "L1PA2_dup3766" "L1PA2_dup3629"
## [973] "L1PA2_dup2876" "L1PA2_dup382" "L1HS_dup1014" "L1PA3_dup9702"
## [977] "L1HS_dup376" "L1HS_dup1437" "L1PA2_dup2127" "L1PA2_dup4478"
## [981] "L1PA2_dup4389" "L1PA2_dup2444" "L1PA3_dup1943" "L1HS_dup1284"
## [985] "L1PA2_dup2537" "L1PA2_dup3118" "L1HS_dup1491" "L1PA2_dup472"
## [989] "L1HS_dup1501" "L1PA2_dup1049" "L1PA2_dup2261" "L1PA3_dup7288"
## [993] "L1PA3_dup4687" "L1PA3_dup3291" "L1PA3_dup8891" "L1HS_dup600"
## [997] "L1PA3_dup10011" "L1HS_dup35" "L1PA2_dup1023" "L1HS_dup1286"
## [1001] "L1PA3_dup5207" "L1PA2_dup1248" "L1PA2_dup3930" "L1PA2_dup3292"
## [1005] "L1PA2_dup4901" "L1PA2_dup1050" "L1PA3_dup5544" "L1PA3_dup4349"
## [1009] "L1PA2_dup2271" "L1PA2_dup1978" "L1HS_dup1576" "L1PA2_dup365"
## [1013] "L1PA2_dup423" "L1PA2_dup4618" "L1HS_dup743" "L1HS_dup1019"
## [1017] "L1PA2_dup4262" "L1PA2_dup3283" "L1PA3_dup7605" "L1PA2_dup4776"
## [1021] "L1HS_dup1478" "L1PA2_dup4237" "L1HS_dup1357" "L1PA3_dup1337"
## [1025] "L1PA2_dup4421" "L1PA3_dup6436" "L1PA2_dup2408" "L1PA2_dup1968"
## [1029] "L1PA3_dup5057" "L1HS_dup803" "L1PA3_dup2620" "L1PA2_dup4441"
## [1033] "L1PA2_dup4335" "L1PA2_dup98" "L1PA3_dup8310" "L1PA2_dup1953"
## [1037] "L1PA2_dup1805" "L1PA3_dup1114" "L1PA2_dup4030" "L1PA2_dup1058"
## [1041] "L1PA3_dup4708" "L1PA3_dup5534" "L1PA3_dup1269" "L1PA3_dup3968"
## [1045] "L1PA3_dup7550" "L1PA2_dup1778" "L1PA2_dup3405" "L1PA3_dup1264"
## [1049] "L1PA3_dup9473" "L1PA3_dup4688" "L1PA2_dup3607" "L1PA2_dup3881"
## [1053] "L1PA3_dup4709" "L1PA3_dup1800" "L1PA3_dup9095" "L1PA2_dup3437"
## [1057] "L1PA3_dup5238" "L1PA3_dup8007" "L1PA3_dup978" "L1PA3_dup165"
## [1061] "L1PA2_dup71" "L1PA3_dup2393" "L1PA2_dup142" "L1PA3_dup358"
## [1065] "L1PA2_dup1933" "L1PA3_dup2357" "L1PA2_dup662" "L1PA2_dup585"
## [1069] "L1PA3_dup2760" "L1PA2_dup2680" "L1HS_dup455" "L1PA3_dup527"
## [1073] "L1HS_dup514" "L1PA2_dup1462" "L1PA2_dup410" "L1PA2_dup1379"
## [1077] "L1PA3_dup561" "L1PA3_dup872" "L1PA3_dup2039" "L1PA3_dup4804"
## [1081] "L1PA2_dup2988" "L1PA3_dup3941" "L1PA3_dup5121" "L1PA3_dup5514"
## [1085] "L1PA3_dup3757" "L1PA3_dup3758" "L1PA2_dup4367" "L1PA3_dup128"
## [1089] "L1PA3_dup124" "L1HS_dup337" "L1PA3_dup4122" "L1PA3_dup907"
## [1093] "L1PA3_dup9280" "L1PA2_dup200" "L1PA3_dup7637" "L1PA2_dup559"
## [1097] "L1PA2_dup2860" "L1PA3_dup4902" "L1PA2_dup2289" "L1PA3_dup4885"
## [1101] "L1PA2_dup2791" "L1PA2_dup635" "L1PA3_dup2272" "L1PA3_dup6385"
## [1105] "L1PA2_dup4620" "L1PA3_dup5680" "L1PA2_dup2909" "L1HS_dup1462"
## [1109] "L1PA3_dup10740" "L1PA2_dup3771" "L1PA2_dup2164" "L1PA2_dup1298"
## [1113] "L1PA3_dup4891" "L1PA2_dup3589" "L1PA3_dup7862" "L1PA2_dup1752"
## [1117] "L1PA3_dup7963" "L1PA3_dup7472" "L1PA3_dup1710" "L1PA3_dup4401"
## [1121] "L1PA2_dup3805" "L1HS_dup788" "L1PA2_dup221" "L1PA2_dup3736"
## [1125] "L1PA3_dup7821" "L1HS_dup1330" "L1PA3_dup6002" "L1PA3_dup7951"
## [1129] "L1HS_dup191" "L1PA3_dup3507" "L1PA3_dup3168" "L1PA3_dup4391"
## [1133] "L1PA2_dup663" "L1HS_dup1536" "L1HS_dup632" "L1PA2_dup526"
## [1137] "L1PA2_dup1418" "L1PA2_dup2720" "L1PA3_dup7237" "L1PA3_dup1010"
## [1141] "L1PA3_dup1311" "L1PA3_dup4994" "L1PA2_dup922" "L1PA2_dup1230"
## [1145] "L1PA3_dup2593" "L1PA3_dup8663" "L1PA3_dup2919" "L1PA3_dup4277"
## [1149] "L1PA3_dup2557" "L1PA2_dup2245" "L1PA2_dup927" "L1PA3_dup373"
## [1153] "L1PA3_dup529" "L1PA3_dup1756" "L1PA2_dup1272" "L1PA2_dup791"
## [1157] "L1PA3_dup10119" "L1PA3_dup10285" "L1PA3_dup8525" "L1PA3_dup6966"
## [1161] "L1PA3_dup6730" "L1HS_dup596" "L1PA2_dup737" "L1PA2_dup4838"
## [1165] "L1PA2_dup513" "L1PA3_dup9430" "L1PA3_dup8571" "L1PA3_dup2204"
## [1169] "L1PA3_dup8520" "L1PA3_dup4603" "L1PA3_dup3102" "L1HS_dup449"
## [1173] "L1PA3_dup2721" "L1PA2_dup2385" "L1PA3_dup8872" "L1PA3_dup3863"
## [1177] "L1PA2_dup1760" "L1PA3_dup5510" "L1PA3_dup2662" "L1PA3_dup9734"
## [1181] "L1PA3_dup6147" "L1HS_dup1182" "L1HS_dup138" "L1PA2_dup3531"
## [1185] "L1PA3_dup7470" "L1PA3_dup6550" "L1PA2_dup234" "L1PA3_dup761"
## [1189] "L1PA3_dup2517" "L1PA3_dup5337" "L1PA3_dup6573" "L1PA2_dup37"
## [1193] "L1PA2_dup3136" "L1HS_dup800" "L1PA2_dup3664" "L1PA3_dup6434"
## [1197] "L1PA2_dup378" "L1PA3_dup398" "L1PA3_dup2744" "L1PA2_dup530"
## [1201] "L1PA3_dup2413" "L1PA3_dup748" "L1PA3_dup4492" "L1PA2_dup130"
## [1205] "L1PA3_dup6036" "L1PA2_dup2091" "L1PA3_dup9021" "L1PA3_dup2551"
## [1209] "L1PA2_dup848" "L1PA3_dup6457" "L1PA3_dup4888" "L1PA3_dup10686"
## [1213] "L1PA3_dup8903" "L1HS_dup240" "L1PA2_dup196" "L1PA3_dup1"
## [1217] "L1PA3_dup4118" "L1PA2_dup4403" "L1PA3_dup1651" "L1PA3_dup10297"
## [1221] "L1PA3_dup9256"
asap_heatmap_snRNA(region = c("SN"),
tes = data_TE_annotation$TE_id,
return_df = F, group_rows = c("type"), gaps_row = length(heatmap_sn_HERV_order),
breaks = seq(0,15,length.out = 52), index_row_reorder = c(heatmap_sn_HERV_order,heatmap_sn_L1_order),
order_cols_groups = order_cols_celltype,
data = TE_data, group_cols = c("celltype"),
title = "SN HERVs + L1s: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
exclude_clusters = c(6, 7))

## $heatmap
##
## $order_cols
## [1] "AA_ASAP129_ctrl_NP22-37_SN_1" "AA_ASAP118_PD_NP22-55_SN_1"
## [3] "DA792_ASAP51_ctrl_NP19-36_SN_1" "AA_ASAP137_PD_NP23-21_SN_1"
## [5] "DA487_ASAP8_ctrl_PT231_SN_1" "DA479_ASAP7_ctrl_NP16-21_SN_2"
## [7] "DA433_ASAP5_ctrl_NP16-161_SN_2" "DA431_ASAP4_PD_P74_SN_2"
## [9] "DA784_ASAP46_ctrl_NP17-256_SN_2" "DA475_ASAP2_PD_NP16-25_SN_2"
## [11] "AA_ASAP129_ctrl_NP22-37_SN_2" "AA_ASAP118_PD_NP22-55_SN_2"
## [13] "AA_ASAP99_ctrl_NP16-284_SN_2" "DA782_ASAP41_PD_NP19-108_SN_2"
## [15] "AA_ASAP133_PD_NP17-232_SN_2" "AA_ASAP132_PD_NP16-285_SN_2"
## [17] "DA796_ASAP57_ctrl_NP19-45_SN_2" "AA_ASAP137_PD_NP23-21_SN_2"
## [19] "DA794_ASAP54_ctrl_NP19-37_SN_2" "DA792_ASAP51_ctrl_NP19-36_SN_2"
## [21] "AA_ASAP101_PD_NP21-57_SN_2" "DA489_ASAP3_PD_P73_SN_2"
## [23] "AA_ASAP103_PD_NP21-217_SN_2" "AA_ASAP102_PD_NP21-208_SN_2"
## [25] "DA511_ASAP21_PD_NP16-269_SN_2" "MJ_ASAP6_ctrl_NP16-164_SN_2"
## [27] "AA_ASAP104_ctrl_NP16-119_SN_2" "DA429_ASAP1_PD_NP16-162_SN_2"
## [29] "AA_ASAP135_PD_NP19-137_SN_2" "DA487_ASAP8_ctrl_PT231_SN_2"
## [31] "AA_ASAP127_ctrl_NP19-218_SN_2" "AA_ASAP108_ctrl_NP18-148_SN_2"
## [33] "AA_ASAP134_PD_NP19-91_SN_2" "DA473_ASAP38_PD_NP19-23_SN_2"
## [35] "AA_ASAP105_ctrl_NP16-293_SN_2" "AA_ASAP132_PD_NP16-285_SN_3"
## [37] "AA_ASAP133_PD_NP17-232_SN_3" "DA796_ASAP57_ctrl_NP19-45_SN_3"
## [39] "AA_ASAP103_PD_NP21-217_SN_3" "DA511_ASAP21_PD_NP16-269_SN_3"
## [41] "AA_ASAP101_PD_NP21-57_SN_3" "AA_ASAP102_PD_NP21-208_SN_3"
## [43] "DA473_ASAP38_PD_NP19-23_SN_3" "AA_ASAP105_ctrl_NP16-293_SN_3"
## [45] "AA_ASAP108_ctrl_NP18-148_SN_3" "DA794_ASAP54_ctrl_NP19-37_SN_3"
## [47] "DA792_ASAP51_ctrl_NP19-36_SN_3" "DA431_ASAP4_PD_P74_SN_3"
## [49] "AA_ASAP127_ctrl_NP19-218_SN_3" "AA_ASAP136_PD_NP21-04_SN_3"
## [51] "MJ_ASAP6_ctrl_NP16-164_SN_3" "DA479_ASAP7_ctrl_NP16-21_SN_3"
## [53] "DA475_ASAP2_PD_NP16-25_SN_3" "DA433_ASAP5_ctrl_NP16-161_SN_3"
## [55] "AA_ASAP129_ctrl_NP22-37_SN_3" "DA489_ASAP3_PD_P73_SN_3"
## [57] "AA_ASAP137_PD_NP23-21_SN_3" "AA_ASAP135_PD_NP19-137_SN_3"
## [59] "DA487_ASAP8_ctrl_PT231_SN_3" "AA_ASAP99_ctrl_NP16-284_SN_3"
## [61] "DA429_ASAP1_PD_NP16-162_SN_3" "AA_ASAP134_PD_NP19-91_SN_3"
## [63] "AA_ASAP118_PD_NP22-55_SN_3" "DA784_ASAP46_ctrl_NP17-256_SN_3"
## [65] "AA_ASAP104_ctrl_NP16-119_SN_3" "DA782_ASAP41_PD_NP19-108_SN_3"
## [67] "AA_ASAP136_PD_NP21-04_SN_5" "DA431_ASAP4_PD_P74_SN_5"
## [69] "AA_ASAP129_ctrl_NP22-37_SN_5" "AA_ASAP127_ctrl_NP19-218_SN_5"
## [71] "MJ_ASAP6_ctrl_NP16-164_SN_5" "DA473_ASAP38_PD_NP19-23_SN_5"
## [73] "AA_ASAP108_ctrl_NP18-148_SN_5" "AA_ASAP132_PD_NP16-285_SN_5"
## [75] "DA487_ASAP8_ctrl_PT231_SN_5" "DA792_ASAP51_ctrl_NP19-36_SN_5"
## [77] "DA782_ASAP41_PD_NP19-108_SN_5" "DA479_ASAP7_ctrl_NP16-21_SN_5"
## [79] "DA796_ASAP57_ctrl_NP19-45_SN_5" "DA784_ASAP46_ctrl_NP17-256_SN_5"
## [81] "AA_ASAP99_ctrl_NP16-284_SN_5" "AA_ASAP105_ctrl_NP16-293_SN_5"
## [83] "DA429_ASAP1_PD_NP16-162_SN_5" "AA_ASAP137_PD_NP23-21_SN_5"
## [85] "AA_ASAP101_PD_NP21-57_SN_5" "AA_ASAP103_PD_NP21-217_SN_5"
## [87] "DA489_ASAP3_PD_P73_SN_5" "DA511_ASAP21_PD_NP16-269_SN_5"
## [89] "DA475_ASAP2_PD_NP16-25_SN_5" "AA_ASAP135_PD_NP19-137_SN_5"
## [91] "AA_ASAP104_ctrl_NP16-119_SN_5" "DA433_ASAP5_ctrl_NP16-161_SN_5"
## [93] "AA_ASAP102_PD_NP21-208_SN_5" "DA794_ASAP54_ctrl_NP19-37_SN_5"
## [95] "AA_ASAP118_PD_NP22-55_SN_5" "AA_ASAP133_PD_NP17-232_SN_5"
## [97] "AA_ASAP134_PD_NP19-91_SN_5" "AA_ASAP134_PD_NP19-91_SN_4"
## [99] "DA431_ASAP4_PD_P74_SN_4" "DA487_ASAP8_ctrl_PT231_SN_4"
## [101] "DA473_ASAP38_PD_NP19-23_SN_4" "AA_ASAP129_ctrl_NP22-37_SN_4"
## [103] "AA_ASAP108_ctrl_NP18-148_SN_4" "AA_ASAP137_PD_NP23-21_SN_4"
## [105] "AA_ASAP102_PD_NP21-208_SN_4" "AA_ASAP104_ctrl_NP16-119_SN_4"
## [107] "AA_ASAP127_ctrl_NP19-218_SN_4" "AA_ASAP101_PD_NP21-57_SN_4"
## [109] "AA_ASAP103_PD_NP21-217_SN_4" "DA489_ASAP3_PD_P73_SN_4"
## [111] "DA511_ASAP21_PD_NP16-269_SN_4" "MJ_ASAP6_ctrl_NP16-164_SN_4"
## [113] "DA782_ASAP41_PD_NP19-108_SN_4" "AA_ASAP118_PD_NP22-55_SN_4"
## [115] "DA429_ASAP1_PD_NP16-162_SN_4" "DA792_ASAP51_ctrl_NP19-36_SN_4"
## [117] "AA_ASAP133_PD_NP17-232_SN_4" "AA_ASAP135_PD_NP19-137_SN_4"
## [119] "DA433_ASAP5_ctrl_NP16-161_SN_4" "DA475_ASAP2_PD_NP16-25_SN_4"
## [121] "DA794_ASAP54_ctrl_NP19-37_SN_4"
##
## $order_rows
## [1] "HERV_dup277" "HERV_dup38" "HERV_dup183" "HERV_dup2278"
## [5] "HERV_dup909" "HERV_dup276" "HERV_dup3033" "HERV_dup1243"
## [9] "HERV_dup1731" "HERV_dup1236" "HERV_dup2607" "HERV_dup54"
## [13] "HERV_dup670" "HERV_dup671" "HERV_dup1437" "HERV_dup1778"
## [17] "HERV_dup2524" "HERV_dup3118" "HERV_dup2631" "HERV_dup417"
## [21] "HERV_dup2772" "HERV_dup1638" "HERV_dup184" "HERV_dup1661"
## [25] "HERV_dup2942" "HERV_dup2967" "HERV_dup471" "HERV_dup2290"
## [29] "HERV_dup1201" "HERV_dup916" "HERV_dup2383" "HERV_dup194"
## [33] "HERV_dup2834" "HERV_dup1658" "HERV_dup1662" "HERV_dup1433"
## [37] "HERV_dup975" "HERV_dup724" "HERV_dup1413" "HERV_dup1381"
## [41] "HERV_dup1304" "HERV_dup1605" "HERV_dup1926" "HERV_dup2391"
## [45] "HERV_dup846" "HERV_dup409" "HERV_dup2801" "HERV_dup27"
## [49] "HERV_dup243" "HERV_dup2480" "HERV_dup1470" "HERV_dup2733"
## [53] "HERV_dup3100" "HERV_dup3239" "HERV_dup882" "HERV_dup703"
## [57] "HERV_dup3270" "HERV_dup3171" "HERV_dup662" "HERV_dup2555"
## [61] "HERV_dup2530" "HERV_dup1383" "HERV_dup1195" "HERV_dup1285"
## [65] "HERV_dup1081" "HERV_dup1891" "HERV_dup1416" "HERV_dup851"
## [69] "HERV_dup1082" "HERV_dup899" "HERV_dup3358" "HERV_dup1953"
## [73] "HERV_dup1587" "HERV_dup1526" "HERV_dup1184" "HERV_dup2635"
## [77] "HERV_dup1222" "HERV_dup2797" "HERV_dup599" "HERV_dup433"
## [81] "HERV_dup3187" "HERV_dup407" "HERV_dup2603" "HERV_dup389"
## [85] "HERV_dup2604" "HERV_dup1156" "HERV_dup2778" "HERV_dup3335"
## [89] "HERV_dup1268" "HERV_dup118" "HERV_dup573" "HERV_dup1245"
## [93] "HERV_dup127" "HERV_dup1804" "HERV_dup2149" "HERV_dup2529"
## [97] "HERV_dup1108" "HERV_dup1005" "HERV_dup2378" "HERV_dup2907"
## [101] "HERV_dup728" "HERV_dup736" "HERV_dup577" "HERV_dup1979"
## [105] "HERV_dup2264" "HERV_dup2356" "HERV_dup870" "HERV_dup2804"
## [109] "HERV_dup1071" "HERV_dup331" "HERV_dup935" "HERV_dup1972"
## [113] "HERV_dup1327" "HERV_dup1656" "HERV_dup2566" "HERV_dup1532"
## [117] "HERV_dup3154" "HERV_dup2972" "HERV_dup356" "HERV_dup2548"
## [121] "HERV_dup692" "HERV_dup2130" "HERV_dup2100" "HERV_dup517"
## [125] "HERV_dup3694" "HERV_dup2353" "HERV_dup487" "HERV_dup3519"
## [129] "HERV_dup355" "HERV_dup3394" "HERV_dup3286" "HERV_dup1316"
## [133] "HERV_dup1307" "HERV_dup1401" "HERV_dup2632" "HERV_dup894"
## [137] "HERV_dup3406" "HERV_dup3131" "HERV_dup508" "HERV_dup1036"
## [141] "HERV_dup665" "HERV_dup1491" "HERV_dup419" "HERV_dup591"
## [145] "HERV_dup2320" "HERV_dup2843" "HERV_dup2183" "HERV_dup572"
## [149] "HERV_dup977" "HERV_dup185" "HERV_dup1208" "HERV_dup1253"
## [153] "HERV_dup1556" "HERV_dup201" "HERV_dup2647" "HERV_dup1378"
## [157] "HERV_dup1073" "HERV_dup2324" "HERV_dup441" "HERV_dup3182"
## [161] "HERV_dup3606" "HERV_dup446" "HERV_dup115" "HERV_dup2941"
## [165] "HERV_dup3189" "HERV_dup3015" "HERV_dup1752" "HERV_dup2242"
## [169] "HERV_dup3284" "HERV_dup2878" "HERV_dup388" "HERV_dup1093"
## [173] "HERV_dup2735" "HERV_dup1047" "HERV_dup1017" "HERV_dup1733"
## [177] "HERV_dup981" "HERV_dup3210" "HERV_dup3037" "HERV_dup2646"
## [181] "HERV_dup1668" "HERV_dup1730" "HERV_dup3143" "HERV_dup746"
## [185] "HERV_dup2936" "HERV_dup1440" "HERV_dup772" "HERV_dup735"
## [189] "HERV_dup530" "HERV_dup250" "HERV_dup1520" "HERV_dup2949"
## [193] "HERV_dup1933" "HERV_dup1932" "HERV_dup966" "HERV_dup1667"
## [197] "HERV_dup1948" "HERV_dup398" "HERV_dup369" "HERV_dup554"
## [201] "HERV_dup1389" "HERV_dup2857" "HERV_dup1350" "HERV_dup120"
## [205] "HERV_dup381" "HERV_dup1366" "HERV_dup133" "HERV_dup3179"
## [209] "HERV_dup2187" "HERV_dup3013" "HERV_dup3031" "HERV_dup1210"
## [213] "HERV_dup1302" "HERV_dup1248" "HERV_dup2663" "HERV_dup634"
## [217] "HERV_dup1046" "HERV_dup1962" "HERV_dup551" "HERV_dup3044"
## [221] "HERV_dup1187" "HERV_dup2152" "HERV_dup1557" "HERV_dup2879"
## [225] "HERV_dup1228" "HERV_dup177" "HERV_dup1412" "HERV_dup2939"
## [229] "HERV_dup152" "HERV_dup1112" "HERV_dup180" "HERV_dup1212"
## [233] "HERV_dup3108" "HERV_dup2141" "HERV_dup1213" "HERV_dup565"
## [237] "HERV_dup850" "HERV_dup3016" "HERV_dup2823" "HERV_dup1869"
## [241] "HERV_dup2464" "HERV_dup3215" "HERV_dup1757" "HERV_dup2481"
## [245] "HERV_dup586" "HERV_dup3408" "HERV_dup357" "HERV_dup2518"
## [249] "HERV_dup739" "HERV_dup443" "HERV_dup1823" "HERV_dup3607"
## [253] "HERV_dup2217" "HERV_dup509" "HERV_dup2655" "HERV_dup3212"
## [257] "HERV_dup2894" "HERV_dup1500" "HERV_dup450" "HERV_dup29"
## [261] "HERV_dup1724" "HERV_dup3319" "HERV_dup1239" "HERV_dup3430"
## [265] "HERV_dup3481" "HERV_dup314" "HERV_dup613" "HERV_dup884"
## [269] "HERV_dup39" "HERV_dup1629" "HERV_dup1295" "HERV_dup2557"
## [273] "HERV_dup2129" "HERV_dup1453" "HERV_dup1218" "HERV_dup1958"
## [277] "HERV_dup1049" "HERV_dup2706" "HERV_dup1003" "HERV_dup1851"
## [281] "HERV_dup2441" "HERV_dup1931" "HERV_dup321" "HERV_dup3219"
## [285] "HERV_dup1459" "HERV_dup3137" "HERV_dup1131" "HERV_dup3063"
## [289] "HERV_dup930" "HERV_dup2620" "HERV_dup2886" "HERV_dup3073"
## [293] "HERV_dup570" "HERV_dup1415" "HERV_dup982" "HERV_dup2680"
## [297] "HERV_dup492" "HERV_dup86" "HERV_dup2192" "HERV_dup1639"
## [301] "HERV_dup2747" "HERV_dup23" "HERV_dup732" "HERV_dup682"
## [305] "HERV_dup710" "HERV_dup1934" "HERV_dup2602" "HERV_dup1374"
## [309] "HERV_dup1403" "HERV_dup293" "HERV_dup568" "HERV_dup578"
## [313] "HERV_dup2875" "HERV_dup400" "HERV_dup2728" "HERV_dup17"
## [317] "HERV_dup1438" "HERV_dup348" "HERV_dup2809" "HERV_dup3248"
## [321] "HERV_dup2034" "HERV_dup2415" "HERV_dup399" "HERV_dup3505"
## [325] "HERV_dup1640" "HERV_dup1089" "HERV_dup2303" "HERV_dup3588"
## [329] "HERV_dup1943" "HERV_dup3507" "HERV_dup1278" "HERV_dup2561"
## [333] "HERV_dup831" "HERV_dup1513" "HERV_dup2945" "HERV_dup1514"
## [337] "HERV_dup3181" "HERV_dup1242" "HERV_dup729" "HERV_dup1579"
## [341] "HERV_dup469" "HERV_dup3217" "HERV_dup1272" "HERV_dup2653"
## [345] "HERV_dup21" "HERV_dup84" "HERV_dup3673" "HERV_dup1331"
## [349] "HERV_dup1279" "HERV_dup3008" "HERV_dup57" "HERV_dup1099"
## [353] "HERV_dup803" "HERV_dup1653" "HERV_dup1920" "HERV_dup1720"
## [357] "HERV_dup2905" "HERV_dup1356" "HERV_dup2536" "HERV_dup2128"
## [361] "HERV_dup2840" "HERV_dup2977" "HERV_dup251" "HERV_dup3363"
## [365] "HERV_dup2159" "HERV_dup1303" "HERV_dup2743" "HERV_dup5"
## [369] "HERV_dup350" "HERV_dup2562" "HERV_dup2937" "HERV_dup2533"
## [373] "HERV_dup3366" "HERV_dup773" "HERV_dup1321" "HERV_dup1613"
## [377] "HERV_dup1914" "HERV_dup890" "HERV_dup1351" "HERV_dup36"
## [381] "HERV_dup2963" "HERV_dup949" "HERV_dup1203" "HERV_dup3388"
## [385] "HERV_dup2900" "HERV_dup1569" "HERV_dup3231" "HERV_dup214"
## [389] "HERV_dup1512" "HERV_dup1875" "HERV_dup2855" "HERV_dup151"
## [393] "HERV_dup2848" "HERV_dup1417" "HERV_dup1890" "HERV_dup913"
## [397] "HERV_dup3580" "HERV_dup3522" "HERV_dup3220" "HERV_dup2812"
## [401] "HERV_dup34" "HERV_dup2550" "HERV_dup1090" "HERV_dup26"
## [405] "HERV_dup3287" "HERV_dup94" "HERV_dup129" "HERV_dup1371"
## [409] "HERV_dup2179" "HERV_dup1847" "HERV_dup1001" "HERV_dup1846"
## [413] "HERV_dup990" "HERV_dup2891" "HERV_dup1298" "HERV_dup2599"
## [417] "HERV_dup1334" "HERV_dup1269" "HERV_dup2736" "HERV_dup1755"
## [421] "HERV_dup2785" "HERV_dup2027" "HERV_dup386" "HERV_dup1717"
## [425] "HERV_dup2166" "HERV_dup112" "HERV_dup1050" "HERV_dup1339"
## [429] "HERV_dup3148" "HERV_dup2334" "HERV_dup632" "HERV_dup1611"
## [433] "HERV_dup758" "HERV_dup799" "HERV_dup301" "HERV_dup2002"
## [437] "HERV_dup1750" "HERV_dup3105" "HERV_dup2964" "HERV_dup2319"
## [441] "HERV_dup1052" "HERV_dup1029" "HERV_dup1614" "HERV_dup933"
## [445] "HERV_dup2436" "HERV_dup3050" "HERV_dup488" "HERV_dup776"
## [449] "HERV_dup344" "HERV_dup203" "HERV_dup1107" "HERV_dup1935"
## [453] "HERV_dup1390" "HERV_dup1364" "HERV_dup2033" "HERV_dup1346"
## [457] "HERV_dup110" "HERV_dup723" "HERV_dup1868" "HERV_dup2897"
## [461] "HERV_dup58" "HERV_dup968" "HERV_dup108" "HERV_dup3117"
## [465] "HERV_dup1324" "HERV_dup3328" "HERV_dup3416" "HERV_dup3140"
## [469] "HERV_dup2250" "HERV_dup2163" "HERV_dup852" "HERV_dup2500"
## [473] "HERV_dup2235" "HERV_dup873" "HERV_dup482" "HERV_dup2273"
## [477] "HERV_dup1345" "HERV_dup2188" "HERV_dup3124" "HERV_dup1080"
## [481] "HERV_dup1447" "HERV_dup2041" "HERV_dup3341" "HERV_dup626"
## [485] "HERV_dup3459" "HERV_dup1780" "HERV_dup2934" "HERV_dup2112"
## [489] "HERV_dup3251" "HERV_dup3107" "HERV_dup329" "HERV_dup434"
## [493] "HERV_dup2896" "HERV_dup640" "HERV_dup1617" "HERV_dup934"
## [497] "HERV_dup1719" "HERV_dup377" "HERV_dup1707" "HERV_dup1541"
## [501] "HERV_dup1240" "HERV_dup597" "HERV_dup3351" "HERV_dup904"
## [505] "HERV_dup2282" "HERV_dup1923" "HERV_dup2476" "HERV_dup900"
## [509] "HERV_dup1333" "HERV_dup2422" "HERV_dup2379" "HERV_dup1655"
## [513] "HERV_dup956" "HERV_dup1235" "HERV_dup65" "HERV_dup1598"
## [517] "HERV_dup2739" "HERV_dup3020" "HERV_dup18" "HERV_dup1449"
## [521] "HERV_dup3355" "HERV_dup1319" "HERV_dup1322" "HERV_dup2019"
## [525] "HERV_dup1657" "HERV_dup202" "HERV_dup2847" "HERV_dup2525"
## [529] "HERV_dup282" "HERV_dup218" "HERV_dup1007" "HERV_dup467"
## [533] "HERV_dup2366" "HERV_dup272" "HERV_dup2404" "HERV_dup2093"
## [537] "HERV_dup2298" "HERV_dup1663" "HERV_dup777" "HERV_dup2784"
## [541] "HERV_dup2292" "HERV_dup2365" "HERV_dup562" "HERV_dup1362"
## [545] "HERV_dup1359" "HERV_dup3198" "HERV_dup1596" "HERV_dup1802"
## [549] "HERV_dup2111" "HERV_dup2261" "HERV_dup2176" "HERV_dup1282"
## [553] "HERV_dup1703" "HERV_dup380" "HERV_dup292" "HERV_dup1102"
## [557] "HERV_dup1004" "HERV_dup2266" "HERV_dup1694" "HERV_dup3266"
## [561] "HERV_dup2769" "HERV_dup939" "HERV_dup1382" "HERV_dup612"
## [565] "HERV_dup468" "HERV_dup470" "HERV_dup1670" "HERV_dup1982"
## [569] "HERV_dup1315" "HERV_dup1917" "HERV_dup1702" "HERV_dup1671"
## [573] "HERV_dup290" "HERV_dup1888" "HERV_dup2803" "HERV_dup2598"
## [577] "HERV_dup2106" "HERV_dup2623" "HERV_dup2915" "HERV_dup2966"
## [581] "HERV_dup2877" "HERV_dup249" "HERV_dup2182" "HERV_dup2012"
## [585] "HERV_dup3410" "HERV_dup1209" "HERV_dup2856" "HERV_dup1973"
## [589] "HERV_dup2438" "HERV_dup1484" "HERV_dup2914" "HERV_dup1357"
## [593] "HERV_dup872" "HERV_dup1002" "HERV_dup954" "HERV_dup600"
## [597] "HERV_dup2412" "HERV_dup927" "HERV_dup2961" "HERV_dup3390"
## [601] "HERV_dup1283" "HERV_dup1308" "HERV_dup3417" "HERV_dup1297"
## [605] "HERV_dup2085" "HERV_dup384" "HERV_dup1317" "HERV_dup3365"
## [609] "HERV_dup2651" "HERV_dup2962" "HERV_dup1281" "HERV_dup1048"
## [613] "HERV_dup1114" "HERV_dup2985" "HERV_dup300" "HERV_dup1394"
## [617] "HERV_dup1255" "HERV_dup209" "HERV_dup3226" "HERV_dup969"
## [621] "HERV_dup2158" "HERV_dup1756" "HERV_dup926" "HERV_dup3342"
## [625] "HERV_dup3343" "HERV_dup2376" "HERV_dup2589" "HERV_dup2588"
## [629] "HERV_dup93" "HERV_dup980" "HERV_dup474" "HERV_dup3529"
## [633] "HERV_dup2695" "HERV_dup1940" "HERV_dup2789" "HERV_dup2299"
## [637] "HERV_dup2134" "HERV_dup61" "HERV_dup880" "HERV_dup2643"
## [641] "HERV_dup1358" "HERV_dup1" "HERV_dup37" "HERV_dup1889"
## [645] "HERV_dup717" "HERV_dup288" "HERV_dup2841" "HERV_dup1000"
## [649] "HERV_dup1669" "HERV_dup1701" "HERV_dup302" "HERV_dup3375"
## [653] "HERV_dup731" "HERV_dup1758" "HERV_dup3423" "HERV_dup2662"
## [657] "HERV_dup2491" "HERV_dup265" "HERV_dup1456" "HERV_dup1232"
## [661] "HERV_dup1310" "HERV_dup3379" "HERV_dup1309" "HERV_dup518"
## [665] "HERV_dup3418" "HERV_dup1708" "HERV_dup1079" "HERV_dup3252"
## [669] "HERV_dup3174" "HERV_dup2752" "HERV_dup3357" "HERV_dup379"
## [673] "HERV_dup2381" "HERV_dup2838" "HERV_dup2880" "HERV_dup940"
## [677] "HERV_dup614" "HERV_dup979" "HERV_dup2902" "HERV_dup1749"
## [681] "L1PA3_dup7792" "L1PA3_dup5047" "L1PA3_dup2662" "L1PA3_dup2683"
## [685] "L1PA2_dup741" "L1PA3_dup4408" "L1PA2_dup2496" "L1PA2_dup994"
## [689] "L1PA2_dup4651" "L1PA3_dup8328" "L1PA2_dup39" "L1PA3_dup1264"
## [693] "L1PA3_dup9734" "L1PA3_dup6160" "L1HS_dup831" "L1PA3_dup4688"
## [697] "L1PA3_dup9473" "L1PA3_dup6112" "L1PA3_dup4487" "L1PA2_dup3881"
## [701] "L1PA3_dup9255" "L1PA2_dup4596" "L1PA2_dup3405" "L1HS_dup916"
## [705] "L1PA3_dup5057" "L1PA2_dup2271" "L1PA3_dup1988" "L1PA3_dup6584"
## [709] "L1PA2_dup4775" "L1PA2_dup3607" "L1PA3_dup3306" "L1PA2_dup559"
## [713] "L1PA3_dup2039" "L1PA2_dup4367" "L1PA3_dup1952" "L1PA3_dup2954"
## [717] "L1PA3_dup9430" "L1PA3_dup10344" "L1PA3_dup4884" "L1PA2_dup326"
## [721] "L1PA3_dup1723" "L1PA3_dup128" "L1PA2_dup4618" "L1PA2_dup1746"
## [725] "L1HS_dup379" "L1PA2_dup2343" "L1PA3_dup5510" "L1PA2_dup2430"
## [729] "L1PA3_dup3502" "L1PA3_dup7432" "L1PA3_dup5418" "L1HS_dup155"
## [733] "L1PA2_dup1760" "L1PA2_dup2581" "L1PA2_dup2863" "L1PA3_dup5238"
## [737] "L1PA2_dup1653" "L1PA2_dup413" "L1PA3_dup8173" "L1PA3_dup6317"
## [741] "L1PA3_dup9840" "L1PA3_dup8891" "L1HS_dup270" "L1PA2_dup589"
## [745] "L1PA3_dup10525" "L1PA3_dup8506" "L1PA2_dup423" "L1PA2_dup98"
## [749] "L1PA2_dup3484" "L1PA3_dup10096" "L1HS_dup376" "L1PA3_dup5355"
## [753] "L1PA3_dup5358" "L1PA3_dup5540" "L1PA2_dup4776" "L1PA3_dup2643"
## [757] "L1PA3_dup1547" "L1PA3_dup3954" "L1PA3_dup2357" "L1PA3_dup3300"
## [761] "L1PA2_dup4309" "L1HS_dup907" "L1PA2_dup1560" "L1PA3_dup5468"
## [765] "L1PA2_dup1058" "L1PA3_dup1428" "L1PA3_dup7316" "L1HS_dup62"
## [769] "L1PA3_dup4668" "L1PA3_dup1554" "L1PA3_dup3509" "L1PA3_dup5745"
## [773] "L1PA2_dup4226" "L1PA2_dup3622" "L1PA2_dup3445" "L1PA3_dup1528"
## [777] "L1PA2_dup16" "L1PA3_dup6966" "L1PA3_dup5928" "L1PA2_dup747"
## [781] "L1PA2_dup1248" "L1PA3_dup6436" "L1PA3_dup6008" "L1HS_dup405"
## [785] "L1PA3_dup2204" "L1PA2_dup4053" "L1PA2_dup3503" "L1PA2_dup4901"
## [789] "L1HS_dup679" "L1HS_dup1286" "L1HS_dup1324" "L1HS_dup90"
## [793] "L1HS_dup1295" "L1PA3_dup8896" "L1PA3_dup6730" "L1PA3_dup3102"
## [797] "L1PA2_dup3042" "L1PA2_dup3283" "L1PA2_dup4045" "L1PA3_dup1027"
## [801] "L1PA3_dup1026" "L1PA2_dup1331" "L1PA3_dup3729" "L1PA2_dup1978"
## [805] "L1PA2_dup684" "L1PA2_dup2168" "L1PA3_dup6871" "L1PA3_dup6523"
## [809] "L1HS_dup225" "L1PA3_dup1770" "L1HS_dup1014" "L1PA2_dup4522"
## [813] "L1PA2_dup4639" "L1PA2_dup4441" "L1HS_dup803" "L1PA2_dup1476"
## [817] "L1HS_dup1514" "L1PA2_dup4389" "L1PA2_dup798" "L1PA2_dup1177"
## [821] "L1PA2_dup109" "L1PA3_dup9866" "L1PA2_dup1398" "L1PA2_dup3426"
## [825] "L1HS_dup1437" "L1PA3_dup2620" "L1PA3_dup3484" "L1PA3_dup3291"
## [829] "L1PA3_dup1337" "L1PA2_dup3160" "L1PA2_dup4548" "L1PA2_dup2047"
## [833] "L1PA3_dup3684" "L1HS_dup1342" "L1PA2_dup1463" "L1PA3_dup1463"
## [837] "L1PA2_dup4478" "L1HS_dup1616" "L1HS_dup1393" "L1PA2_dup2180"
## [841] "L1PA2_dup805" "L1PA2_dup4611" "L1PA2_dup3629" "L1PA2_dup2537"
## [845] "L1HS_dup444" "L1HS_dup1491" "L1HS_dup1284" "L1PA3_dup4393"
## [849] "L1HS_dup1501" "L1PA2_dup472" "L1PA2_dup2004" "L1PA3_dup683"
## [853] "L1HS_dup143" "L1PA2_dup4713" "L1PA2_dup382" "L1HS_dup429"
## [857] "L1HS_dup163" "L1HS_dup204" "L1PA2_dup4432" "L1PA2_dup1049"
## [861] "L1HS_dup802" "L1PA2_dup2444" "L1PA2_dup3118" "L1PA2_dup4612"
## [865] "L1PA3_dup3959" "L1PA2_dup2436" "L1PA3_dup7288" "L1HS_dup370"
## [869] "L1PA2_dup4335" "L1PA2_dup2504" "L1PA2_dup4652" "L1PA3_dup8117"
## [873] "L1PA3_dup840" "L1PA3_dup3404" "L1PA3_dup5363" "L1PA2_dup2506"
## [877] "L1PA2_dup2261" "L1HS_dup600" "L1PA2_dup3766" "L1PA3_dup5825"
## [881] "L1PA3_dup1727" "L1PA3_dup1943" "L1PA3_dup10072" "L1PA3_dup638"
## [885] "L1HS_dup466" "L1HS_dup1104" "L1PA2_dup2577" "L1PA2_dup360"
## [889] "L1PA2_dup4378" "L1PA2_dup759" "L1HS_dup1077" "L1PA2_dup726"
## [893] "L1HS_dup811" "L1HS_dup579" "L1PA2_dup3776" "L1PA3_dup1989"
## [897] "L1PA3_dup5544" "L1PA2_dup3292" "L1HS_dup1357" "L1PA2_dup4043"
## [901] "L1PA2_dup2282" "L1PA3_dup7893" "L1PA3_dup345" "L1PA2_dup514"
## [905] "L1PA3_dup3005" "L1HS_dup995" "L1PA2_dup1621" "L1PA3_dup8310"
## [909] "L1PA2_dup4421" "L1PA3_dup8313" "L1PA2_dup2385" "L1PA2_dup1968"
## [913] "L1PA2_dup383" "L1PA2_dup4201" "L1PA2_dup935" "L1PA3_dup2389"
## [917] "L1PA2_dup2295" "L1HS_dup35" "L1PA3_dup5866" "L1PA3_dup9373"
## [921] "L1PA2_dup2729" "L1HS_dup1478" "L1PA3_dup3586" "L1PA2_dup3003"
## [925] "L1PA3_dup10176" "L1PA3_dup3153" "L1PA2_dup3930" "L1PA3_dup3763"
## [929] "L1PA2_dup4262" "L1PA3_dup10043" "L1PA3_dup5207" "L1PA2_dup358"
## [933] "L1PA2_dup4688" "L1PA2_dup678" "L1PA2_dup1023" "L1PA2_dup4237"
## [937] "L1PA2_dup365" "L1PA2_dup4686" "L1HS_dup1576" "L1PA2_dup2254"
## [941] "L1PA2_dup4762" "L1PA2_dup675" "L1PA3_dup1550" "L1PA3_dup4596"
## [945] "L1PA3_dup10011" "L1PA3_dup9856" "L1HS_dup111" "L1HS_dup1243"
## [949] "L1PA2_dup2876" "L1PA2_dup4791" "L1HS_dup1473" "L1PA3_dup9722"
## [953] "L1PA2_dup949" "L1PA2_dup3439" "L1PA3_dup9702" "L1PA2_dup307"
## [957] "L1PA2_dup4936" "L1HS_dup622" "L1HS_dup1339" "L1HS_dup87"
## [961] "L1PA3_dup247" "L1PA3_dup4603" "L1PA3_dup3323" "L1PA2_dup4430"
## [965] "L1PA3_dup3950" "L1HS_dup124" "L1PA2_dup3773" "L1PA2_dup219"
## [969] "L1PA2_dup4454" "L1PA2_dup1490" "L1HS_dup1020" "L1PA3_dup5886"
## [973] "L1PA3_dup5106" "L1PA2_dup629" "L1HS_dup1005" "L1PA2_dup1426"
## [977] "L1PA2_dup1050" "L1PA2_dup4196" "L1PA3_dup10531" "L1PA3_dup6387"
## [981] "L1PA3_dup5594" "L1HS_dup743" "L1PA2_dup2408" "L1PA3_dup7605"
## [985] "L1PA2_dup2089" "L1HS_dup649" "L1PA3_dup5927" "L1PA3_dup6884"
## [989] "L1HS_dup879" "L1PA3_dup2755" "L1PA2_dup1112" "L1PA3_dup7947"
## [993] "L1PA3_dup1328" "L1PA3_dup3863" "L1HS_dup1019" "L1PA3_dup1046"
## [997] "L1PA2_dup3425" "L1PA2_dup732" "L1PA2_dup1992" "L1PA2_dup2127"
## [1001] "L1PA2_dup4528" "L1HS_dup787" "L1PA3_dup9202" "L1PA2_dup2565"
## [1005] "L1HS_dup244" "L1PA3_dup1647" "L1PA2_dup1078" "L1PA3_dup9946"
## [1009] "L1PA3_dup6692" "L1PA3_dup7840" "L1PA3_dup400" "L1PA3_dup4349"
## [1013] "L1PA3_dup7550" "L1PA3_dup1269" "L1PA2_dup1953" "L1PA2_dup2155"
## [1017] "L1PA3_dup4708" "L1PA2_dup4030" "L1PA3_dup7864" "L1PA3_dup5534"
## [1021] "L1PA2_dup3615" "L1PA2_dup1805" "L1PA3_dup1114" "L1PA3_dup3968"
## [1025] "L1PA3_dup3880" "L1PA3_dup165" "L1PA2_dup71" "L1PA3_dup2393"
## [1029] "L1PA3_dup4259" "L1PA3_dup1279" "L1PA2_dup3579" "L1PA2_dup1375"
## [1033] "L1PA3_dup8420" "L1PA2_dup727" "L1PA3_dup358" "L1PA2_dup4074"
## [1037] "L1PA3_dup4687" "L1PA3_dup9095" "L1PA2_dup142" "L1HS_dup1182"
## [1041] "L1PA2_dup1770" "L1PA2_dup1933" "L1PA2_dup635" "L1PA3_dup761"
## [1045] "L1PA3_dup6434" "L1PA3_dup4885" "L1PA3_dup561" "L1HS_dup800"
## [1049] "L1PA3_dup8520" "L1PA3_dup4902" "L1PA2_dup2289" "L1PA2_dup2860"
## [1053] "L1PA2_dup2791" "L1PA3_dup872" "L1PA3_dup9280" "L1PA2_dup200"
## [1057] "L1PA3_dup124" "L1PA3_dup6929" "L1PA3_dup2517" "L1PA3_dup9998"
## [1061] "L1PA3_dup5337" "L1PA3_dup3307" "L1PA3_dup978" "L1PA3_dup8007"
## [1065] "L1HS_dup514" "L1PA3_dup6385" "L1PA2_dup663" "L1HS_dup1536"
## [1069] "L1HS_dup632" "L1PA2_dup585" "L1PA2_dup2680" "L1PA2_dup1462"
## [1073] "L1PA2_dup1749" "L1PA3_dup8571" "L1PA3_dup5514" "L1HS_dup788"
## [1077] "L1HS_dup455" "L1HS_dup1330" "L1PA2_dup221" "L1PA3_dup7951"
## [1081] "L1PA2_dup1379" "L1PA3_dup2272" "L1HS_dup191" "L1PA3_dup7472"
## [1085] "L1PA2_dup3736" "L1HS_dup337" "L1PA2_dup2988" "L1PA3_dup4804"
## [1089] "L1PA3_dup3941" "L1PA2_dup3742" "L1PA3_dup1311" "L1PA3_dup6573"
## [1093] "L1PA2_dup3437" "L1PA3_dup6147" "L1PA3_dup2557" "L1PA3_dup4492"
## [1097] "L1PA2_dup1272" "L1PA3_dup7237" "L1PA2_dup791" "L1PA3_dup1010"
## [1101] "L1PA3_dup10119" "L1PA2_dup922" "L1PA2_dup1230" "L1PA3_dup2593"
## [1105] "L1PA3_dup8663" "L1PA3_dup10285" "L1PA3_dup4994" "L1PA2_dup526"
## [1109] "L1PA3_dup1756" "L1PA2_dup2245" "L1PA3_dup373" "L1PA2_dup927"
## [1113] "L1PA3_dup2919" "L1PA3_dup4391" "L1PA3_dup4888" "L1PA2_dup4403"
## [1117] "L1PA2_dup4620" "L1PA2_dup3771" "L1PA2_dup1298" "L1PA3_dup5121"
## [1121] "L1PA3_dup1710" "L1PA3_dup4891" "L1PA3_dup4401" "L1PA3_dup6002"
## [1125] "L1PA3_dup7821" "L1PA2_dup3589" "L1PA2_dup3805" "L1PA2_dup410"
## [1129] "L1PA3_dup7963" "L1PA2_dup2909" "L1PA3_dup5680" "L1PA3_dup10740"
## [1133] "L1PA2_dup1752" "L1HS_dup1462" "L1PA3_dup10297" "L1PA2_dup2164"
## [1137] "L1PA3_dup907" "L1PA3_dup4122" "L1PA3_dup7637" "L1PA2_dup2969"
## [1141] "L1PA2_dup3531" "L1PA3_dup3507" "L1PA3_dup3168" "L1PA2_dup4440"
## [1145] "L1PA2_dup4714" "L1HS_dup138" "L1PA2_dup530" "L1PA3_dup7470"
## [1149] "L1PA2_dup234" "L1PA3_dup8522" "L1PA3_dup6550" "L1PA3_dup2744"
## [1153] "L1PA3_dup398" "L1PA2_dup378" "L1PA3_dup7862" "L1PA3_dup3757"
## [1157] "L1PA3_dup3758" "L1PA3_dup8525" "L1PA2_dup37" "L1PA2_dup595"
## [1161] "L1PA2_dup3136" "L1HS_dup596" "L1PA3_dup8872" "L1HS_dup449"
## [1165] "L1PA3_dup2721" "L1PA2_dup4838" "L1PA2_dup737" "L1PA2_dup513"
## [1169] "L1PA2_dup130" "L1PA3_dup6036" "L1PA2_dup4905" "L1PA3_dup6347"
## [1173] "L1PA2_dup3664" "L1PA3_dup2413" "L1PA3_dup2551" "L1PA3_dup9021"
## [1177] "L1PA2_dup2091" "L1PA2_dup1778" "L1PA3_dup748" "L1PA2_dup2720"
## [1181] "L1PA3_dup2760" "L1PA2_dup662" "L1PA3_dup529" "L1PA3_dup527"
## [1185] "L1PA2_dup1418" "L1PA3_dup1937" "L1HS_dup948" "L1PA3_dup4709"
## [1189] "L1PA3_dup1800" "L1PA3_dup9256" "L1PA2_dup848" "L1PA3_dup6457"
## [1193] "L1PA3_dup4277" "L1HS_dup240" "L1PA2_dup196" "L1PA3_dup8903"
## [1197] "L1PA3_dup1651" "L1PA3_dup4118" "L1PA3_dup1" "L1PA3_dup10686"
Tables of stacked heatmaps
If there is anyone interested, I’ve also saved these matrices to keep
the order in which they are shown in figure (return_df = T)
to ./ASAP/data/ASAP_PMDBS_snRNAseq/results/tables/.
heatmap_pfc <- asap_heatmap_snRNA(region = c("PFC"),
tes = data_TE_annotation$TE_id,
return_df = T, group_rows = c("type"), gaps_row = length(heatmap_pfc_HERV_order),
breaks = seq(0,15,length.out = 52), index_row_reorder = c(heatmap_pfc_HERV_order,heatmap_pfc_L1_order),
data = TE_data, group_cols = c("celltype"),
order_cols_groups = order_cols_celltype,
title = "PFC HERVs + L1s: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
exclude_clusters = c(6, 7))
heatmap_put <- asap_heatmap_snRNA(region = c("PUT"),
tes = data_TE_annotation$TE_id,
return_df = T, group_rows = c("type"), gaps_row = length(heatmap_put_HERV_order),
breaks = seq(0,15,length.out = 52), index_row_reorder = c(heatmap_put_HERV_order,heatmap_put_L1_order),
data = TE_data, group_cols = c("celltype"),
order_cols_groups = order_cols_celltype,
title = "PUT HERVs + L1s: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
exclude_clusters = c(6, 7))
heatmap_amy <- asap_heatmap_snRNA(region = c("AMY"),
tes = data_TE_annotation$TE_id,
return_df = T, group_rows = c("type"), gaps_row = length(heatmap_amy_HERV_order),
breaks = seq(0,15,length.out = 52), index_row_reorder = c(heatmap_amy_HERV_order,heatmap_amy_L1_order),
data = TE_data, group_cols = c("celltype"),
order_cols_groups = order_cols_celltype,
title = "AMY HERVs + L1s: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
exclude_clusters = c(6, 7))
heatmap_sn <- asap_heatmap_snRNA(region = c("SN"),
tes = data_TE_annotation$TE_id,
return_df = T, group_rows = c("type"), gaps_row = length(heatmap_sn_HERV_order),
breaks = seq(0,15,length.out = 52), index_row_reorder = c(heatmap_sn_HERV_order,heatmap_sn_L1_order),
data = TE_data, group_cols = c("celltype"),
order_cols_groups = order_cols_celltype,
title = "SN HERVs + L1s: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
exclude_clusters = c(6, 7))
heatmap_sn$norm_counts <- merge(TE_data$te_counts[,c("Geneid", "Chr", "Start", "End", "Strand", "Length")], heatmap_sn$norm_counts, by.y="TE_id", by.x="Geneid")
heatmap_pfc$norm_counts <- merge(TE_data$te_counts[,c("Geneid", "Chr", "Start", "End", "Strand", "Length")], heatmap_pfc$norm_counts, by.y="TE_id", by.x="Geneid")
heatmap_put$norm_counts <- merge(TE_data$te_counts[,c("Geneid", "Chr", "Start", "End", "Strand", "Length")], heatmap_put$norm_counts, by.y="TE_id", by.x="Geneid")
heatmap_amy$norm_counts <- merge(TE_data$te_counts[,c("Geneid", "Chr", "Start", "End", "Strand", "Length")], heatmap_amy$norm_counts, by.y="TE_id", by.x="Geneid")
write.table(heatmap_sn$norm_counts, "/Volumes/MyPassport/ASAP/data/ASAP_PMDBS_snRNAseq/results/tables/heatmap_matrix_SN_FL_HERVs_L1HS_PA3_expressed_bulk_celltype_cluster.tab", sep = ",", quote = F, col.names = T, row.names = F)
write.table(heatmap_pfc$norm_counts, "/Volumes/MyPassport//ASAP/data/ASAP_PMDBS_snRNAseq/results/tables/heatmap_matrix_PFC_FL_HERVs_L1HS_PA3_expressed_bulk_celltype_cluster.tab", sep = ",", quote = F, col.names = T, row.names = F)
write.table(heatmap_put$norm_counts, "/Volumes/MyPassport//ASAP/data/ASAP_PMDBS_snRNAseq/results/tables/heatmap_matrix_PUT_FL_HERVs_L1HS_PA3_expressed_bulk_celltype_cluster.tab", sep = ",", quote = F, col.names = T, row.names = F)
write.table(heatmap_amy$norm_counts, "/Volumes/MyPassport//ASAP/data/ASAP_PMDBS_snRNAseq/results/tables/heatmap_matrix_AMY_FL_HERVs_L1HS_PA3_expressed_bulk_celltype_cluster.tab", sep = ",", quote = F, col.names = T, row.names = F)
Box plots of L1 expression from heatmaps
These matrices also helped to make the boxplots from the same figures
(to compare expression between neurons, glia and microglia). We just
need to retrieve them per element type (L1/HERVs).
heatmap_pfc_L1 <- asap_heatmap_snRNA(region = c("PFC"),
tes = data_TE_annotation[which(data_TE_annotation$type == "L1"),"TE_id"],
return_df = T,
breaks = seq(0,15,length.out = 52),
data = TE_data, group_cols = c("celltype"),
order_cols_groups = order_cols_celltype,
title = "PFC L1s: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
exclude_clusters = c(6, 7))
heatmap_put_L1 <- asap_heatmap_snRNA(region = c("PUT"),
tes = data_TE_annotation[which(data_TE_annotation$type == "L1"),"TE_id"],
return_df = T,
breaks = seq(0,15,length.out = 52),
data = TE_data, group_cols = c("celltype"),
order_cols_groups = order_cols_celltype,
title = "PUT L1s: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
exclude_clusters = c(6, 7))
heatmap_sn_L1 <- asap_heatmap_snRNA(region = c("SN"),
tes = data_TE_annotation[which(data_TE_annotation$type == "L1"),"TE_id"],
return_df = T,
breaks = seq(0,15,length.out = 52),
data = TE_data, group_cols = c("celltype"),
order_cols_groups = order_cols_celltype,
title = "SN L1s: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
exclude_clusters = c(6, 7))
heatmap_amy_L1 <- asap_heatmap_snRNA(region = c("AMY"),
tes = data_TE_annotation[which(data_TE_annotation$type == "L1"),"TE_id"],
return_df = T,
breaks = seq(0,15,length.out = 52),
data = TE_data, group_cols = c("celltype"),
order_cols_groups = order_cols_celltype,
title = "AMY L1s: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
exclude_clusters = c(6, 7))
merge(data.frame(L1_sum = colMeans(heatmap_pfc_L1$norm_counts[,-ncol(heatmap_pfc_L1$norm_counts)])),
heatmap_pfc_L1$samplesheet, by="row.names") %>%
mutate(celltype_simple = fct_relevel(celltype_simple,c("Neurons","Glia","Microglia"))) %>%
ggplot(aes(x=celltype_simple, y=L1_sum, color = celltype_simple)) + geom_jitter(height = 0, width = 0.4) +
geom_boxplot(width=0.5, alpha = 0.5, outliers = F) +
theme_bw() + theme(legend.position = "None") + scale_color_manual(values = c("Neurons" = "#a0dbb0",
"Glia" = "#a1a8e6",
"Microglia" = "grey")) +
labs(y="log2(Pseudobulk normalized\nmean expression)", x="", color="") + stat_compare_means(comparisons = list(c("Neurons", "Microglia"), c("Neurons", "Glia"), c("Microglia", "Glia")), method = "t.test") + ggtitle("PFC >6kbp L1HS-PA3 ")

merge(data.frame(L1_sum = colMeans(heatmap_put_L1$norm_counts[,-ncol(heatmap_put_L1$norm_counts)])),
heatmap_put_L1$samplesheet, by="row.names") %>%
mutate(celltype_simple = fct_relevel(celltype_simple,c("Neurons","Glia","Microglia"))) %>%
ggplot(aes(x=celltype_simple, y=L1_sum, color = celltype_simple)) + geom_jitter(height = 0, width = 0.4) +
geom_boxplot(width=0.5, alpha = 0.5, outliers = F) +
theme_bw() + theme(legend.position = "None") + scale_color_manual(values = c("Neurons" = "#a0dbb0",
"Glia" = "#a1a8e6",
"Microglia" = "grey")) +
labs(y="log2(Pseudobulk normalized\nmean expression)", x="", color="") + stat_compare_means(comparisons = list(c("Neurons", "Microglia"), c("Neurons", "Glia"), c("Microglia", "Glia")), method = "t.test") + ggtitle("PUT >6kbp L1HS-PA3 ")

merge(data.frame(L1_sum = colMeans(heatmap_sn_L1$norm_counts[,-ncol(heatmap_sn_L1$norm_counts)])),
heatmap_sn_L1$samplesheet, by="row.names") %>%
mutate(celltype_simple = fct_relevel(celltype_simple,c("Neurons","Glia","Microglia"))) %>%
ggplot(aes(x=celltype_simple, y=L1_sum, color = celltype_simple)) + geom_jitter(height = 0, width = 0.4) +
geom_boxplot(width=0.5, alpha = 0.5, outliers = F) +
theme_bw() + theme(legend.position = "None") + scale_color_manual(values = c("Neurons" = "#a0dbb0",
"Glia" = "#a1a8e6",
"Microglia" = "grey")) +
labs(y="log2(Pseudobulk normalized\nmean expression)", x="", color="") + stat_compare_means(comparisons = list(c("Neurons", "Microglia"), c("Neurons", "Glia"), c("Microglia", "Glia")), method = "t.test") + ggtitle("SN >6kbp L1HS-PA3 ")

merge(data.frame(L1_sum = colMeans(heatmap_amy_L1$norm_counts[,-ncol(heatmap_amy_L1$norm_counts)])),
heatmap_amy_L1$samplesheet, by="row.names") %>%
mutate(celltype_simple = fct_relevel(celltype_simple,c("Neurons","Glia","Microglia"))) %>%
ggplot(aes(x=celltype_simple, y=L1_sum, color = celltype_simple)) + geom_jitter(height = 0, width = 0.4) +
geom_boxplot(width=0.5, alpha = 0.5, outliers = F) +
theme_bw() + theme(legend.position = "None") + scale_color_manual(values = c("Neurons" = "#a0dbb0",
"Glia" = "#a1a8e6",
"Microglia" = "grey")) +
labs(y="log2(Pseudobulk normalized\nmean expression)", x="", color="") + stat_compare_means(comparisons = list(c("Neurons", "Microglia"), c("Neurons", "Glia"), c("Microglia", "Glia")), method = "t.test") + ggtitle("AMY >6kbp L1HS-PA3 ")

Box plots of HERV expression from heatmaps
Same method for HERVs!
heatmap_amy_HERV <- asap_heatmap_snRNA(region = c("AMY"),
tes = data_TE_annotation[which(data_TE_annotation$type == "HERV"),"TE_id"],
return_df = T,
breaks = seq(0,15,length.out = 60),
data = TE_data, group_cols = c("celltype"),
order_cols_groups = order_cols_celltype,
title = "AMY HERVs: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
exclude_clusters = c(6, 7))
heatmap_pfc_HERV <- asap_heatmap_snRNA(region = c("PFC"),
tes = data_TE_annotation[which(data_TE_annotation$type == "HERV"),"TE_id"],
return_df = T,
breaks = seq(0,15,length.out = 60),
data = TE_data, group_cols = c("celltype"),
order_cols_groups = order_cols_celltype,
title = "PFC HERVs: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
exclude_clusters = c(6, 7))
heatmap_put_HERV <- asap_heatmap_snRNA(region = c("PUT"),
tes = data_TE_annotation[which(data_TE_annotation$type == "HERV"),"TE_id"],
return_df = T,
breaks = seq(0,15,length.out = 60),
data = TE_data, group_cols = c("celltype"),
order_cols_groups = order_cols_celltype,
title = "PUT HERVs: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
exclude_clusters = c(6, 7))
heatmap_sn_HERV <- asap_heatmap_snRNA(region = c("SN"),
tes = data_TE_annotation[which(data_TE_annotation$type == "HERV"),"TE_id"],
return_df = T,
breaks = seq(0,15,length.out = 60),
data = TE_data, group_cols = c("celltype"),
order_cols_groups = order_cols_celltype,
title = "SN HERVs: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
exclude_clusters = c(6, 7))
merge(data.frame(HERV_sum = colMeans(heatmap_pfc_HERV$norm_counts[,-ncol(heatmap_pfc_HERV$norm_counts)])),
heatmap_pfc_HERV$samplesheet, by="row.names") %>%
mutate(celltype_simple = fct_relevel(celltype_simple,c("Neurons","Glia","Microglia"))) %>%
ggplot(aes(x=celltype_simple, y=HERV_sum, color = celltype_simple)) + geom_jitter(height = 0, width = 0.4) +
geom_boxplot(width=0.5, alpha = 0.5, outliers = F) +
theme_bw() + theme(legend.position = "None") + scale_color_manual(values = c("Neurons" = "#a0dbb0",
"Glia" = "#a1a8e6",
"Microglia" = "grey")) +
labs(y="log2(Pseudobulk normalized\nmean expression)", x="", color="") + stat_compare_means(comparisons = list(c("Neurons", "Microglia"), c("Neurons", "Glia"), c("Microglia", "Glia")), method = "t.test") + ggtitle("PFC HERVs ")

merge(data.frame(HERV_sum = colMeans(heatmap_put_HERV$norm_counts[,-ncol(heatmap_put_HERV$norm_counts)])),
heatmap_put_HERV$samplesheet, by="row.names") %>%
mutate(celltype_simple = fct_relevel(celltype_simple,c("Neurons","Glia","Microglia"))) %>%
ggplot(aes(x=celltype_simple, y=HERV_sum, color = celltype_simple)) + geom_jitter(height = 0, width = 0.4) +
geom_boxplot(width=0.5, alpha = 0.5, outliers = F) +
theme_bw() + theme(legend.position = "None") + scale_color_manual(values = c("Neurons" = "#a0dbb0",
"Glia" = "#a1a8e6",
"Microglia" = "grey")) +
labs(y="log2(Pseudobulk normalized\nmean expression)", x="", color="") + stat_compare_means(comparisons = list(c("Neurons", "Microglia"), c("Neurons", "Glia"), c("Microglia", "Glia")), method = "t.test") + ggtitle("PUT HERVs ")

merge(data.frame(HERV_sum = colMeans(heatmap_sn_HERV$norm_counts[,-ncol(heatmap_sn_HERV$norm_counts)])),
heatmap_sn_HERV$samplesheet, by="row.names") %>%
mutate(celltype_simple = fct_relevel(celltype_simple,c("Neurons","Glia","Microglia"))) %>%
ggplot(aes(x=celltype_simple, y=HERV_sum, color = celltype_simple)) + geom_jitter(height = 0, width = 0.4) +
geom_boxplot(width=0.5, alpha = 0.5, outliers = F) +
theme_bw() + theme(legend.position = "None") + scale_color_manual(values = c("Neurons" = "#a0dbb0",
"Glia" = "#a1a8e6",
"Microglia" = "grey")) +
labs(y="log2(Pseudobulk normalized\nmean expression)", x="", color="") + stat_compare_means(comparisons = list(c("Neurons", "Microglia"), c("Neurons", "Glia"), c("Microglia", "Glia")), method = "t.test") + ggtitle("SN HERVs ")

merge(data.frame(HERV_sum = colMeans(heatmap_amy_HERV$norm_counts[,-ncol(heatmap_amy_HERV$norm_counts)])),
heatmap_amy_HERV$samplesheet, by="row.names") %>%
mutate(celltype_simple = fct_relevel(celltype_simple,c("Neurons","Glia","Microglia"))) %>%
ggplot(aes(x=celltype_simple, y=HERV_sum, color = celltype_simple)) + geom_jitter(height = 0, width = 0.4) +
geom_boxplot(width=0.5, alpha = 0.5, outliers = F) +
theme_bw() + theme(legend.position = "None") + scale_color_manual(values = c("Neurons" = "#a0dbb0",
"Glia" = "#a1a8e6",
"Microglia" = "grey")) +
labs(y="log2(Pseudobulk normalized\nmean expression)", x="", color="") + stat_compare_means(comparisons = list(c("Neurons", "Microglia"), c("Neurons", "Glia"), c("Microglia", "Glia")), method = "t.test") + ggtitle("AMY HERVs ")
